U.S. patent application number 12/144573 was filed with the patent office on 2008-10-16 for high throughput processing system and method of using.
This patent application is currently assigned to IRM LLC. Invention is credited to Kristina Marie Burow, Jeremy S. Caldwell, Robert Charles Downs, Scott Allan Lesley, James Kevin Mainquist, Andrew J. Meyer, Daniel G. Sipes, Mark Richard Weselak.
Application Number | 20080253927 12/144573 |
Document ID | / |
Family ID | 22906219 |
Filed Date | 2008-10-16 |
United States Patent
Application |
20080253927 |
Kind Code |
A1 |
Burow; Kristina Marie ; et
al. |
October 16, 2008 |
HIGH THROUGHPUT PROCESSING SYSTEM AND METHOD OF USING
Abstract
The present invention provides a system and method for high
throughput processing using sample holders. The system has a
plurality of work perimeters, with a rotational robot preferably
associated with each work perimeter. At least one transfer station
area is provided between adjacent work perimeters to facilitate
robotic transfer of sample holders from one work perimeter to
another area. Each work perimeter typically includes a plurality of
defined station locations, with each station location positioned to
be accessible by the robot associated with that area. In addition,
each station location is typically configured to receive a device,
such as an automated instrument or a holding nest. Device
components are arranged at selected station locations according to
specific application requirements to provide a flexible, robust,
reliable, and accurate high throughput processing system.
Inventors: |
Burow; Kristina Marie;
(Chicago, IL) ; Caldwell; Jeremy S.; (La Jolla,
CA) ; Downs; Robert Charles; (La Jolla, CA) ;
Lesley; Scott Allan; (San Diego, CA) ; Mainquist;
James Kevin; (San Diego, CA) ; Meyer; Andrew J.;
(Solana Beach, CA) ; Sipes; Daniel G.; (San Diego,
CA) ; Weselak; Mark Richard; (San Diego, CA) |
Correspondence
Address: |
GENOMICS INSTITUTE OF THE;NOVARTIS RESEARCH FOUNDATION
10675 JOHN JAY HOPKINS DRIVE, SUITE E225
SAN DIEGO
CA
92121-1127
US
|
Assignee: |
IRM LLC
Hamilton
BM
|
Family ID: |
22906219 |
Appl. No.: |
12/144573 |
Filed: |
June 23, 2008 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09981313 |
Oct 15, 2001 |
7390458 |
|
|
12144573 |
|
|
|
|
60240361 |
Oct 13, 2000 |
|
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Current U.S.
Class: |
422/64 |
Current CPC
Class: |
G01N 2035/0427 20130101;
Y10T 436/2575 20150115; G01N 2015/1006 20130101; B01J 2219/00587
20130101; G01N 35/028 20130101; G01N 35/025 20130101; Y10T
436/114165 20150115; B01J 2219/00691 20130101; G01N 2500/20
20130101; B01L 9/523 20130101; B01J 2219/0072 20130101; G01N
2500/10 20130101; G01N 2035/1037 20130101; G01N 2035/00306
20130101; G01N 2035/00366 20130101; G01N 35/04 20130101; G01N
35/1074 20130101; B01J 2219/00707 20130101; B01L 2300/0893
20130101; B01L 2300/0829 20130101; B01J 2219/00689 20130101; G01N
35/026 20130101; G01N 2035/0405 20130101; Y02A 50/30 20180101; G01N
35/0099 20130101 |
Class at
Publication: |
422/64 |
International
Class: |
G01N 35/10 20060101
G01N035/10 |
Claims
1. A high throughput processing system, the system comprising: (a)
a plurality of rotational robots, wherein each of the rotational
robots has a reach which defines a work perimeter associated with
that rotational robot; (b) at least one device associated with each
of the work perimeters, wherein at least one of the work perimeters
has two or more devices exclusively within the reach of the
rotational robot associated with that work perimeter; (c) one or
more transfer stations associated with at least a first work
perimeter and a second work perimeter, for transferring one or more
samples from the first work perimeter to the second work perimeter;
and (d) storage compartments that provide storage capacity for at
least 350,000 samples.
2. The high throughput processing system of claim 1, wherein the
transfer station transfers the one or more samples by transferring
a sample holder from a first work perimeter to a second work
perimeter.
3. The high throughput processing system of claim 1, wherein the
transfer station comprises a fluid transfer device which transfers
samples from a sample holder in the first work perimeter to a
sample holder in the second work perimeter.
4. The high throughput processing system of claim 1, wherein the
system comprises between 2 and 10 rotational robots.
5. The high throughput processing system of claim 1, wherein the
devices are selected from the group consisting of a fluid transfer
device, a mixer, an incubator, a storage compartment, a
thermocycler, a plate carousel, an automatic sample processor, a
detector, and a replating station.
6. The high throughput processing system of claim 5, wherein one or
more of the devices comprises a fluid transfer device.
7. The high throughput processing system of claim 6, wherein the
fluid transfer device comprises an apparatus selected from the
group consisting of a pin tool, a syringe, and a pump.
8. The high throughput processing system of claim 5, wherein one or
more of the devices comprises an incubator or storage
compartment.
9. The high throughput processing system of claim 1, wherein the
system comprises storage compartments that provide storage capacity
for at least 700,000 samples.
10. The high throughput processing system of claim 9, wherein the
storage compartments provide storage capacity for at least
1,400,000 samples.
11. The high throughput processing system of claim 5, wherein one
or more of the devices comprises a detector which detects one or
more readouts of assay results.
12. The high throughput processing system of claim 1, wherein the
system can perform assays of at least 100,000 samples in one
day.
13. The high throughput processing system of claim 12, wherein the
system can perform assays of at least 350,000 samples in one
day.
14. The high throughput processing system of claim 13, wherein the
system can perform assays of at least 700,000 samples in one
day.
15. The high throughput processing system of claim 1, wherein one
or more of the devices comprises a positioning device that
comprises at least a first alignment member that is positioned to
contact an inner wall of a multiwell plate when the multiwell plate
is in a desired position on the device.
16. The high throughput processing system of claim 15, wherein the
positioning device further comprises a pusher that can move the
multiwell plate in a first direction to bring at least a first
inner wall of the multiwell plate into contact with one or more of
the alignment members.
17. The high throughput processing system of claim 16, wherein the
positioning device further comprises a second pusher that can move
the multiwell plate in a second direction to bring a second inner
wall of the multiwell plate into contact with one or more alignment
members that are positioned to contact the second inner wall of the
multiwell plate when the multiwell plate is in a desired position
on the device.
18. The high throughput processing system of claim 1, further
comprising a controller operably coupled to the high throughput
processing system.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 09/981,313, filed Oct. 15, 2001, now pending, which application
claims benefit of U.S. Provisional Application No. 60/240,361,
filed Oct. 13, 2000, entitled "High Throughput Processing System
and Methods of Using," the disclosures of which are incorporated
herein by reference in their entirety for all purposes.
BACKGROUND OF THE INVENTION
[0002] Automated processing systems are useful in many applications
and fields. For example, automated laboratory systems are used in
biotechnology and biomedical industries, e.g., for producing large
numbers of samples and screening these samples for a desired
property. Such samples include, but are not limited to, chemicals,
cells, cell extracts, or genetic material such as cDNA,
retroviruses, or anti-sense oligonucleotides. To facilitate faster
processing, samples are typically processed together on a
multi-well specimen plate, such as a 384 or 1,536 well plate.
[0003] Automated systems using specimen plates generally provide
faster processing of samples as compared to manual processes. High
throughput automated systems typically involve rapid, repetitive
manipulations of individual elements. One deficiency in existing
technology is that as processing throughputs increase there is a
degradation of reliability.
[0004] One example of an automated processing system is found in
U.S. Pat. No. 5,985,214, which relates to a system having several
workstations. A conveyor transport moves specimen plates holding
samples between the workstations. Accordingly, the specimen plate
moves in a linear fashion from a first processing workstation to
the next sequential processing workstation. To move to any
workstation, a specimen plate is first retrieved from a central
storage rack, and then transported down a long linear track until
the plate reaches one of the several workstations. When the plate
is at the desired workstation, the plate leaves the first linear
track and is placed on a second orthogonal linear track that
presents the plate to an automated instrument. This system,
however, suffers from a lack of flexibility. The plates must
proceed in a linear fashion along the entire track, thus limiting
throughput. Further, once the rack, workstation, and cooperating
transports are in place, it is difficult to reconfigure the system.
In addition, samples in the specimen plates are subjected to an
open and unprotected environment for an extended period of time as
the plates move from the sample racks to the workstations. Thus,
the samples may become impermissibly dry or contaminated.
[0005] Another known automated processing system is described in
U.S. Pat. No. 5,928,952, which relates to a system having a series
of processing units arranged to sequentially receive specimen
plates holding samples or products. In this system, each individual
unit performs a specific task using the specimen plates. Further,
each unit has an associated robotic device for receiving a plate
from an adjacent unit. The system uses plural robots to perform
automated process having several steps. For example, for a unit
performing a step in the process, a robot associated with the unit
retrieves a specimen plate from the previous unit and moves the
specimen plate to the processing position in the unit. When the
unit has completed its step, the robot moves the specimen plate to
where the next robot can retrieve the plate. In such a manner, the
system is cumbersome to operate in a process having many steps and
using several different workstations.
[0006] Disadvantageously, current high throughput processing
systems are limited to unidirectional workflow and inflexible
testing regimes. For example, once the testing samples are
delivered to a workstation in U.S. Pat. No. 5,985,214 or the
interchangeable unit in U.S. Pat. No. 5,928,952, the samples
proceed inexorably from one workstation to the next workstation in
only one direction. Current systems do not allow for a sample to
proceed, for example, from an assaying step, to a dispensing step,
and then back to the previous assaying step. Instead, an entirely
new workstation must be built subsequent to the dispensing step in
order to perform the assay step that was provided two workstations
ago. As each workstation is capable of performing only one
function, every additional step in current systems involves adding
another robot and another workstation, thereby entailing additional
alignment, integration and calibration with the overall system.
[0007] Therefore, there exists a need for an efficient automated
processing system such as a high throughput processing system that
is accurate, reliable, and flexible. The demand for high throughput
systems with decreased reconfiguration needs that are prone to less
contamination and can process samples multi-directionally within
the system is as yet unmet. The present invention provides improved
high throughput processing systems that fulfill these needs and
many others that will be apparent upon complete review of the
following disclosure.
SUMMARY OF THE INVENTION
[0008] The present invention methods and systems for high
throughput processing, e.g., flexible, efficient, and robust high
throughput processing, such as screening of chemical and/or
biochemical libraries. Typically, the systems comprise work
perimeters that are configured for optimum flexibility while
retaining an efficient and precise system. The systems optionally
perform assays of at least about 100,000 samples in about one day,
at least about 350,000 samples in about one day, or at least about
700,000 samples in about one day.
[0009] In one embodiment, a high throughput processing system is
provided. The system typically comprises a plurality of rotational
robots, wherein each of the rotational robots has a reach which
defines a work perimeter associated with that rotational robot.
Typically, at least one device is associated with each of the work
perimeters, and at least one of the work perimeters has two or more
devices exclusively within the reach of the associated rotational
robot. In addition, one or more transfer stations is associated
with at least a first work perimeter and a second work perimeter,
for transferring samples or sample holders from the first work
perimeter to the second work perimeter. The system can transfer
samples along a multi-directional path, or a non-sequential or
non-linear path.
[0010] The systems also typically comprise a plurality of sample
holders, e.g., comprising a plurality of test samples or compounds,
which sample holders are transported between devices and work
perimeters during operation of the system. Typical sample holders
include, but are not limited to, specimen plates, multiwell plates
(1536-well plates, 384-well plates, and/or 96-well plates), petri
dishes, test tube arrays, vials, crucibles, flasks, reaction
vessels, slides, and the like.
[0011] In some embodiments, the sample holders comprise one or more
lids. An example lid of the invention comprises a cover having a
top surface, a bottom surface, and a side. An alignment protrusion
extends from the side of the cover, e.g., positioned to cooperate
with an alignment member of the multiwell plate. In addition, a
sealing perimeter is positioned on the bottom surface of the cover.
The alignment protrusion facilitates aligning the lid to the plate
so that a seal is compressibly received between the sealing
perimeter and a sealing surface of the multiwell plate. The lids
are, in some embodiments, constructed of a heavy material such as
stainless steel. A de-lidding station is also optionally
incorporated into the systems of the invention, at which station a
lid is removed from a sample holder.
[0012] Samples optionally screened or processed in the present
systems comprise chemical or biochemical compounds, nucleic acids,
peptides, polypeptides, proteins, carbohydrates, cells, serum,
phage particles, virions, enzymes, cell extracts, lipids,
antibodies, and the like. For example, one or more library of cDNA
molecules, antisense nucleic acids, double-stranded RNA molecules,
or gene regulatory regions, e.g., operably linked to a reporter
gene, are optionally screened in the present systems. Regulatory
regions in such libraries are optionally derived from genes that
are differentially expressed in a cell depending upon the presence
or absence of a particular stimulus. Combinatorial libraries of
chemical compounds are also optionally screened using the present
systems.
[0013] In addition to the samples described above, a second set of
sample holders are optionally assay holders that comprise
containers and/or reagents for conducting one or more assay. The
assay holders optionally comprise one or more components of an
assay, in which a test sample is added to the assay containers,
e.g., from a first set of sample holders, to determine the effect
of the test samples on the assay. Assays, e.g., cell based assays,
performed in the present systems include, but are not limited to, a
G-protein coupled receptor assay, a kinase assay, a protease assay,
a phosphatase assay, a transcription assay, and the like.
[0014] The rotational robots, e.g., between about 2 and about 10
robots, of the system optionally each comprise one or more grippers
configured to transport the sample holders, which grippers
optionally comprise a sensor structured to determine a location of
the gripper apparatus relative to the object. In addition, the
grippers optionally comprise a deflectable member structured to
couple the gripper apparatus to a robotic member, which deflectable
member is structured to deflect when the gripper apparatus contacts
an item with a force greater than a preset force.
[0015] Devices for use in the system are typically selected from a
fluid transfer device, e.g., a pin tool, a syringe, a pump or the
like, a mixer, an incubator, a storage compartment, a thermocycler,
a plate carousel, an automatic sample processor, a detector, a
replating station, and the like.
[0016] A fluid transfer device is optionally used as a device of
the invention. The fluid transfer devices can, for example,
transfer an aliquot of a test sample from a sample holder that
comprises test samples to an assay sample holder in which an assay
is to be performed. Fluid transfer devices can also dispense
fluids, such as reagents, etc., from a reservoir into one or more
sample holders. The assay holders typically comprise one or more of
living cells, cell extracts, nucleic acids, polypeptides,
antibodies, or chemicals, e.g., for a biochemical, chemical,
biological, microbiological, or cell-based assay.
[0017] Fluid transfer devices of the invention optionally comprise
an array of receptacles, e.g., 96 or 384 receptacles such as
syringes, arranged such that outlets of the receptacles are aligned
with a plurality of wells of one or more multiwell plate. In
another embodiment, a fluid transfer device aspirates a volume of
sample into one or more of the receptacles from a well of a
multiwell plate which is aligned with the outlet of the receptacle.
The device then typically returns a substantial portion of the
volume of the aspirated sample to the well of the multiwell plate,
the returned volume of the liquid being less than the aspirated
volume so that a volume of sample is retained in the receptacle. A
portion of the retained volume of sample is then dispensed, e.g.,
into a well of a second multiwell plate; and any remaining volume
of retained liquid is optionally discarded. When a pin tool is used
as a fluid transfer device, the system can further comprises one or
more wash stations in which the pins are washed between transfers
of fluid from one multiwell plate to another by the pin tool.
Typically, the fluid transfer devices of the invention do not
comprise disposable pipette tips.
[0018] The systems of the invention can include storage
compartments that provide storage capacity for at least about
350,000 samples. In some embodiments, storage is provided for at
least about 700,000 samples, or at least about 1,400,000 samples.
An example storage compartment has a housing that includes a
plurality of doors, which doors close at least one opening disposed
through at least one surface of the housing. At least one movable
shelf is disposed within the housing, which shelf is capable of
aligning with the opening. Each of the plurality of doors is
typically independently accessible by the rotational robot.
[0019] Detectors included in the systems of the invention can
include but are not limited to, a fluorescence detector, a
spectrophotometric detector, a luminescence detector, a
phosphorescence detector, an X-ray detector, a radio-frequency
detector, a bar code reader, a mass spectrometer, a radioactivity
detector, an optical detector, and the like. In some embodiments,
the detector comprises a camera which records images, e.g., digital
images, of the assay results. The resulting images are analyzed,
e.g., at a later date or time, to determine assay results which
indicate a desired effect of a test sample.
[0020] In some embodiments, the sample holders comprise multiwell
plates and one or more of the devices of the system comprise a
positioning device. The positioning device typically comprises at
least a first alignment member that is positioned to contact an
inner wall of the multiwell plate when the multiwell plate is in a
desired position on the device. The positioning device further
comprises a pusher that can move the multiwell plate in a first
direction to bring a first inner wall of the multiwell plate into
contact with one or more of the alignment members.
[0021] The high throughput processing systems of the invention can
also include a controller operably coupled to the system. The
controller typically directs transport of the sample holders
between one or more of the work perimeters or between one or more
of the devices. Operator instructions to program and direct the
system through the controller can optionally be received through a
graphical user interface.
[0022] In another aspect, the present invention provides methods of
defining a process for operation, e.g., on a high throughput
processing system as provided above. The methods typically comprise
creating a plurality of device steps, wherein each device step
instructs one of the one or more devices in the high throughput
processing system. A plurality of move steps are also created. Each
move step instructs at least a first member of the plurality of
rotational robots, e.g., to move one or more of the sample holders
to one of the one or more devices. The device steps and the move
steps are then arranged into a step list, the step list defining an
order for performing the process.
[0023] In another aspect, the present invention provides a method
of transferring a plurality of samples from two or more members of
a first set of multiwell plates to a member of a second set of
multiwell plates. The method typically comprises providing the two
or more members of the first set of multiwell plates, which members
comprise the plurality of samples. In addition, each member
comprises a marker in at least a first well of the multiwell plate.
The plurality of samples and the marker are then transferred from
the members of the first set of multiwell plates to a member of the
second set of multiwell plates; and the location of the marker from
each member of the first set of multiwell plates in the member of
the second set of multiwell plates is determined. Determining the
location of the markers typically comprises visual monitoring or
fluorescent monitoring. For example, each member of the first set
of multiwell plates typically comprises a marker which differs from
the marker in other members of the first set of multiwell plates,
e.g., the markers comprise colored dyes and the markers differ in
the color of the dye and/or the markers comprise fluorescent dyes
and differ in the concentrations of the fluorescent dyes.
[0024] Typically the members of the second set of multiwell plates
have a number of wells that is a whole number multiple of the
number of wells in the members of the first set of multiwell
plates. For example, the samples and markers can be transferred
from four members of the first set of multiwell plates to one
member of the second set of multiwell plates. The first set of
multiwell plates can be, for example, 96-well plates and the second
set of multiwell plates are 384-well plates. Alternatively, the
first set of multiwell plates are 384-well plates or 96-well plates
and the second set of multiwell plates comprises 1536-well plates.
The methods are particularly useful for use with a high throughput
processing system as described herein. Such systems can have, for
example, one type of plate in one work perimeter and a plate having
a different well density in another work perimeter. The plating
methods of the invention allow one to ascertain whether samples are
transferred correctly from one plate to another having a different
well density. Each of these systems and methods are described in
more detail below.
BRIEF DESCRIPTION OF THE FIGURES
[0025] FIG. 1 is a diagram of one example of a high throughput
screening system made in accordance with the present invention.
[0026] FIG. 2 is a diagram of communication links for a high
throughput screening system, e.g., as shown in FIG. 1.
[0027] FIG. 3 is a diagram showing station locations for a high
throughput screening system as shown in FIG. 1.
[0028] FIG. 4 is a block diagram showing software architecture in
accordance with the present invention.
[0029] FIG. 5 illustrates an input screen for defining a step in a
method in accordance with the present invention.
[0030] FIG. 6 illustrates an input screen for defining a move for a
method in accordance with the present invention.
[0031] FIG. 7 is a block diagram illustrating a method of defining
a screen in accordance with the present invention.
[0032] FIG. 8 is a diagram showing station locations of a
non-linear processing system in accordance with the present
invention.
[0033] FIG. 9 illustrates an example high throughput processing
system of the invention.
[0034] FIG. 10 illustrates a communication diagram for the system
shown in FIG. 9.
[0035] FIGS. 11A-D illustrate four 96-well multiwell plates each
comprising a unique marker useful in a replating procedure.
[0036] FIGS. 12A and 12B illustrate higher well density plates that
contain the contents of the four 96 well plates in FIG. 11. FIG.
12A illustrates a 384-well plate and FIG. 12B illustrates a
1536-well plate. Both of the higher well density plates comprise
the markers included in the 96-well plates to indicate the
orientation in which the lower well density plates were transferred
to the higher well density plates.
[0037] FIGS. 13A, B and C illustrate a multiwell plate useful for
precise alignment. FIG. 13A provides a top view, FIG. 13B provides
a side view, and FIG. 13C provides a cross-sectional view.
[0038] FIG. 14 illustrates a positioning device in operation, with
the alignment tabs contacting the inner wall of a microwell plate,
e.g., as shown in FIG. 13.
DETAILED DISCUSSION OF THE INVENTION
[0039] The present invention provides flexible, robust, accurate,
and reliable systems and methods for high throughput processing,
e.g., for screening large numbers of samples. The present invention
alleviates to a great extent the disadvantages of known systems and
methods for screening, analysis, and assembly. For example, the
present system provides multi-directional and non-linear transport
between multiple devices. Accordingly, the present invention
improves the reliability, efficiency, and flexibility of processes
such as high throughput screening and other methods requiring
repetitive manipulations of many individual elements. In addition,
the present invention also provides accurate and quick assembly of
multi-element devices such as medical devices, testing devices,
and/or electronic devices.
[0040] A typical system of the invention comprises a plurality of
rotational robots, each of which is associated with a work
perimeter. Within each work perimeter are a number of devices,
e.g., in various station locations within the work perimeter. In
addition, each station location and/or device is configured to be
accessible by the robot associated with the work perimeter in which
the device is positioned. Typically, at least one work perimeter
has at least two devices that are exclusively within the reach of
the associated rotational robot.
[0041] Transfer stations are also typically included, e.g., between
work perimeters, to facilitate transfer of samples from one work
perimeter to another work perimeter. Furthermore, the whole system
is typically coupled to a controller, e.g., a PC, e.g., for
directing transport of sample holders between devices and directing
processing by those devices. The controllers are typically
configured to receive operator instructions and provide operator
information.
[0042] The systems of the present invention provide flexibility in
multiple ways. For example, the devices used in the systems of the
invention are optionally arranged and positioned at selected
station locations according to the specific requirements of a
desired application. Therefore, the entire system is optionally
tailored to a specific application. In addition, the systems offer
flexibility within each application. For example, the devices in
the system are optionally accessed in any order. The controller is
optionally programmed to access the station locations in any order,
including backtracking to a previously used assaying device. The
random access and random processing provided by the present system
increase throughput and provide a system that is not limited by the
speed of the robot.
[0043] Advantageously, each robot efficiently effects the transfer
of objects between all devices within that robot's work perimeter.
Such close association between each robot and its associated
devices facilitates increased throughput, reliability, and
accuracy. Further, since devices and/or station locations are
easily added, removed, or reconfigured, the systems are highly
flexible. Because each work perimeter preferably contains a
plurality of station locations and/or devices, the overall system
generally requires relatively few work perimeters and associated
robots to perform a given automated process. Accordingly,
transporting samples from one end of the process to the other end
of the process is efficiently and rapidly accomplished. More
advantageously, the present invention provides for
multi-directional transporting within the system. Processing
optionally occurs in any order and is independent of the physical
configuration of the station locations. A system made in accordance
with the present invention performs high throughput processing
quickly, accurately, and with great flexibility, as described in
more detail below.
[0044] For example, a robot in a first work perimeter is optionally
used to transport a sample holder from a storage module, e.g.,
located in a first work perimeter, to a transfer station, from
which transfer station the sample holder is retrieved by a second
robot and transported, e.g., to a second work perimeter.
Alternatively, aliquots of samples in the sample holder can be
transferred at the transfer station to a different sample holder
such as, for example, an assay sample holder. In the second work
perimeter, the sample holder is optionally processed, e.g., by
transporting the sample holder to one or more devices for assaying
the sample. The processing steps are also flexible, in that a
sample is optionally assayed, detected, and then assayed again,
e.g., using a second assaying device or by transporting the sample
holder back to the first assay device. The samples are therefore
optionally allowed to proceed, e.g., from an assaying step, to a
dispensing or detecting step, and back to the assaying step, e.g.,
as directed by a controller, without having to rearrange the entire
system or having an operator manually transport the samples. This
flexibility decreases the need for reconfiguration of the system,
e.g., by moving various devices around, thereby also decreasing the
risk of contamination, e.g., by decreasing the need to handle the
sample containers.
[0045] The samples processed by the systems of the invention are
typically contained in one or more sample holders, e.g., microwell
plates, such as 96, 384, or 1536-well plates. Such samples include,
but are not limited to, genetic material, such as cDNA, chemicals,
biochemicals, serum, cells, cell extracts, nucleic acids, proteins,
enzymes, antibodies, carbohydrates, lipids, blood, inorganic
materials, and the like.
[0046] The systems of the present invention are optionally used for
high throughput screening of samples, e.g., of chemical compounds
against, for example, cells, cell extracts, and/or particular
molecular targets. Accordingly, the invention enables the
identification of novel, bioactive compounds that modulate
biological processes and the identification of cellular and
molecular targets, e.g., of small molecules.
[0047] Chemical compounds identified by high throughput screening
are optionally used as tools for probing and profiling cell
responses and the key molecular entities underlying them. In
addition, chemical compounds identified using the present invention
are optionally used as lead compounds for therapeutic, prognostic
and diagnostic applications. As one example, the present invention
performs efficient, comprehensive, functional pathway scans on
intact cells, thereby screening, e.g., about 100,000 putative
perturbagens per day in a 1536-well format. More preferably the
cell-based, biochemical, or other screening systems of the
invention screen about 350,000 samples in about 1 to about 4 days
with high reliability, and most preferably, about 700,000 samples
in about a day (24 hours). The large capacity ultra high throughput
system also provides reduced costs, e.g., on a per assay basis.
[0048] In another embodiment, the present invention enables high
throughput screening of cDNA oligonucleotides against cells and
sub-cellular targets, e.g., to identify specific molecular targets
associated with particular biochemical pathways. Accordingly, the
present invention permits comprehensive and sensitive functional
profiling of the entire genome of a particular organism.
[0049] In another embodiment, the present invention encompasses
functional screening of antibodies to intracellular targets;
purified affinity-selected 2-hybrid hits; peptides; and both
wild-type and mutant proteins.
[0050] In summary, the present invention provides a high throughput
processing system that is not limited by robot speed or rectilinear
sequential access to devices. The present system provides random
access to and multidirectional transport between multiple devices.
In addition, the system provides reliable and accurate processing,
e.g., for large numbers of samples, e.g., in an ultra-high
throughput manner, e.g., using 1536-well plates. Each component of
the system is discussed in detail below, followed by example
systems and methods of using them.
I. A High Throughput Processing System
[0051] The present invention provides high throughput processing
systems that are useful, for example, for screening large amounts
of target molecules. The systems typically provide an automated
robotic process for handling, mixing, moving, storing, assaying,
and detecting samples. For example, the systems are optionally
designed to carry our assaying, measuring, dispensing, and
detecting steps, e.g., on a plurality of multiwell plates.
[0052] Typically, the systems comprise a plurality of work
perimeters and a plurality of rotational robots, e.g., about 2 to
about 10 robots. Each rotational robot is typically associated with
one or more member of the plurality of work perimeters. For
example, the robots each have a reach which reach defines the work
perimeter associated with that robot. The plurality of work
perimeters and the plurality of rotational robots are configured to
allow transport one or more sample holder along a multi-directional
path, e.g., to provide a flexible transport system for a plurality
of sample holders. In addition, the systems comprise at least one
device associated with each work perimeter. Typically, at least one
of the work perimeters has two or more devices exclusively within
the reach of the associated rotational robot for that work
perimeter. The system is configured to provide non-sequential
transport between the two or more devices, with each device being
accessible by at least one of the rotational robots. To further aid
the transport of the plurality of sample holders, the systems
typically comprise one or more transfer station associated with at
least a first work perimeter and a second work perimeter. The
transfer stations provide transportation of samples (either by
transferring the holders themselves or by transferring aliquots of
samples from one sample holder to another) between work perimeters,
e.g., from the first work perimeter to the second work perimeter.
Each of these elements is described in more detail below.
A. Rotational Robots
[0053] The systems of the invention are typically based around a
plurality of rotational robots. For example, a system of the
invention typically comprises about 2 to about 10 rotational
robots. Preferably, the robots each have a rotational range of
close to about 360 degrees, e.g., they rotate about a rotational
axis a full 360 degrees or almost a full 360 degrees. In addition,
each robot typically adjusts vertically and horizontally to align
with relatively higher or lower work positions.
[0054] Preferably, each rotational robot has a robotic arm that
extends and/or retracts from the robot's rotational axis.
Accordingly, each rotational robot has an associated rotational
reach, e.g., defining how far out from the base the robot operates.
The rotational reach defines a work perimeter, e.g., a circular
work perimeter, for that robot.
[0055] Further, each robotic arm typically has a robotic gripper.
For example, a gripper is used to aid pick up and delivery of
sample holders. The grippers are typically configured to removably
couple with a specimen plate, such as standard 96, 384 or 1,536
well plates. A single gripper mechanism is optionally configured to
accommodate any size plate. Further, the robotic grippers can be
configured to handle other styles of sample holders, including
without limitation, custom sample holders, reaction vessels,
flasks, crucibles, petri dishes, test tube arrays, or vial arrays.
The robotic arms and robotic grippers are typically operated
pneumatically, magnetically, or by other means known in the art.
The grippers typically provide increased reliability, e.g., by use
of pneumatic breakaway grippers. For example, a gripper apparatus
typically comprises a member, e.g., a deflectable member,
structured to couple the gripper apparatus to a robotic member,
which member is structured to deflect when the gripper apparatus
contacts an item with a force greater than a preset force. For
example, see e.g., U.S. Pat. No. 6,592,324.
[0056] In some embodiments, the grippers incorporate optical
sensors, e.g., for detecting which sample holders are being
transported and which direction a particular sample plate should be
inserted into a device, e.g., a plate reader. In addition, a sensor
optionally determines a location of the gripper apparatus relative
to the object to be transported.
[0057] In one embodiment, three Staubli RX-60 robots are used. The
robots are typically pedestal mounted robots, e.g., attached to the
floor or other surface. Staubli RX-60 robots are commercially
available from Staubli Corporation, 201 Parkway West, P.O. Box 189,
Hillside Park, USA-Duncan, South Carolina 29334 (USA). Such robots
are highly accurate and precise to within about one one-thousandth
of an inch. However, any other type of rotational robot is also
optionally used in the robotic system.
[0058] The robots and associated work perimeters and station
locations are typically attached to one or more frames that support
the system. For example, weldments or aluminum extrusion are
optionally used to provide support frames, e.g., with optical table
tops for mounting various devices, e.g., detectors and the like.
Such table tops are typically commercially available, e.g., from
Melles Griot (Irvine Calif.).
[0059] The robots of the system are typically used to transport one
or more sample holder. For example, the robots transfer samples,
e.g., in sample holders, from one work perimeter to another work
perimeter, e.g., via a transfer station. To transfer between
adjacent work perimeters, a first robot retrieves a sample holder
or plate, positions the plate at a transfer station, and then a
robot from an adjacent work perimeter retrieves the plate from the
transfer station. Alternately, the robots are configured to
directly transfer a sample plate from one robot to a second robot.
Preferably, the robots transfer sample holders from device to
device or work perimeter to work perimeter in about 1 to about 10
minutes, more preferably in about 1 to about 5 minutes.
[0060] In addition, the robots transfer sample holders between
station locations within the associated work perimeter of the robot
at issue or between devices. In this manner, the sample holders are
transported to the devices of the invention, e.g., for further
processing, measurement, or detection.
[0061] Because the robots are rotational, i.e., they rotate about
an axis, and are positioned or configured to access an entire work
perimeter, the devices or station locations within the work
perimeter are randomly accessed, e.g., no particular order must be
followed when transporting sample holders to and from the devices.
The robots therefore, provide multidirectional and/or non-linear
transport within the system, allowing sample holders to be brought
directly to the desired station or device without traversing an
entire preset path. This increases the throughput of the system to
beyond that of presently available systems.
B. Work Perimeters
[0062] A "work perimeter," as referred to herein, is an area within
the rotational reach of a robot. The work perimeters of the present
invention typically comprise one or more station location, and
preferably two or more station locations. The station locations are
used to perform various processes, assays, and the like, e.g., on
the samples within a sample plate or holder. Typically, the work
perimeters are defined by the rotational reach of a rotational
robot as described above. For example, FIG. 1 comprises three work
perimeters: area 105, 115, and 125. The work perimeters comprise
the area in which devices and stations are placed and are defined
by the rotational reach of the robots 135, 140, and 145. The
rotational reach areas are shown as circles or ovals but are
optionally any other shape, depending on the reach and extension of
the robot arm. Typically, at least work perimeter has two or more
devices exclusively within the reach of the rotational robot within
that work perimeter. In some embodiments, two or more work
perimeters have two or more devices exclusively within the reach of
the rotational robot within each particular work perimeter. In the
specific embodiment shown in FIG. 1, all three work perimeters each
have two or more devices exclusively within the reach of the
respective robot. The high throughput processing systems of the
invention, in some embodiments, have three or more devices
exclusively within the reach of the rotational robot within that
work perimeter.
[0063] Although FIG. 1 illustrates three work perimeters, the
number of work perimeters is optionally less than or more than
three, depending on specific assay requirements. Typically a work
perimeter is provided for each rotational robot in use and the work
perimeter extends at least as far as the rotational reach of the
robot. The devices associated with each work perimeter can
encompass additional space, for example, as shown as 110, 120 and
130 in FIG. 1. The rotational robot need reach only far enough to
place a sample or sample holder in or on the desired device. For
example, a dispensing device optionally uses up space beyond the
rotational reach of an associated robot, e.g., to accommodate a
pump and or a waste receptacle, yet the robot optionally reaches
only far enough for the dispensing device to receive the sample
holder.
[0064] Each work perimeter is optionally directed to a certain task
or group of tasks, e.g., using the station locations and devices
located within that area. For example, a first work perimeter is
optionally used for storing samples or compounds, while a second
work perimeter is used for processing a sample or group of samples,
e.g., by adding reagents, shaking, heating, incubating, or the
like. A third work perimeter is optionally used for analyzing
and/or detecting the samples once they have been assayed. For
example, a sample is optionally separated into various components,
which are then detected, e.g., using a fluorescent detector.
Alternatively, each work perimeter is directed to a particular type
of assay in a process that involves multiple assays. Although each
work perimeter is generally directed to a particular type of task,
e.g., detection, storage, or the like, the functionality of the
work perimeters is optionally overlapping. For example, a work
perimeter that is generally used for storage, may also be used to
perform a heating step in an assay of interest or some other
processing step.
[0065] One advantage of the present invention is that there is no
particular order that must be followed in transporting samples
between work perimeters, as is the case in many of the existing
systems. Because the system has multidirectional utility, samples
are optionally transported from the first work perimeter to the
second work perimeter and then back to the first area, e.g., for
further processing, prior to detection in a third work perimeter.
This provides an operator the ability to respond, e.g., to results
or information gathered in a first assay, and reprogram the system
accordingly for further processing, e.g., further dilution in a
different work perimeter can be directed during operation if a
sample is found to be too concentrated in a detection step.
[0066] Furthermore, because each work perimeter preferably
accommodates a plurality of devices, and work perimeters are
positioned adjacent each other, an entire high throughput screening
system is optionally configured to fit into a reasonably compact
physical space. For example, a system as shown in FIG. 1 can fit in
an 18'.times.12' space. Fitting into a compact space not only is
efficient from a cost standpoint, but also facilitates efficient
movement of sample holders between work perimeters and from one end
of the system to the other end of the system. By enabling a compact
physical arrangement, the speed and efficiency of the overall
system are increased. Further, because peripheral devices are
compacted into a small physical area, the amount of time a specimen
plate is in transport, and potentially uncovered, is reduced. Thus,
the risks of contamination and undesirable evaporative effects are
reduced. Another advantage of the compactness of the present
invention stems from the ability to enclose the entire system into
a chamber with a well-controlled environment. As such,
environmental effects such as temperature, pressure, humidity, and
particle content can be strictly maintained.
[0067] Each work perimeter typically comprises one or more devices,
e.g., as described below. At least one work perimeter typically has
at least two devices within it that are exclusively within the
reach of the associated robot. Example devices compatible with the
present systems are provided below.
C. Devices
[0068] Typically, each work perimeter in the high throughput
systems of the invention contains a plurality of devices. These
devices can be, for example, automated instruments. Automated
instrument devices are used, e.g., to store, process, and/or detect
samples, e.g., in sample holders. For example, devices are provided
in the work perimeters for storing, assaying, dispensing, and
measuring fluids, reagents, samples, and the like.
[0069] The devices are typically located in or on a station
location, e.g., a platform or table comprising electrical
connections and computer and/or controller connections. The devices
are typically positioned at a station location prior to operation
of the system, however, a device is optionally added to a station
location during operation of the system as well. In addition, the
devices are optionally moved around within a work perimeter, e.g.,
either before operation of the device or upon reconfiguration prior
to using the device for another application. The devices need only
being positioned within a work perimeter, e.g., to be within the
reach of the rotational robot associated with the work perimeter.
If enough station locations are not available, a device is
optionally positioned within the reach of the robot without a
dedicated station location. Typically at least two devices within
at least one work perimeter are exclusively within the reach of the
associated robot.
[0070] Typically each station location in the system contains a
single device, however, multiple devices are optionally positioned
at a single location as well. In addition, the system may comprise
station locations that do not have associated devices or devices
that are not associated with a station location. Unoccupied station
locations are optionally used for storage, temporary holding of
sample holders, or simply not accessed during operation of the
system. In addition, all devices are not necessarily used during
operation of the system. A number of devices are typically
positioned within the station locations of the system prior to
operation. During operation of the system, all of the devices are
optionally used or only a portion of the devices may be used.
Because the rotational robots access each station location
independently, the devices are accessed in any order desired,
including skipping some devices all together and/or repeatedly
accessing one or two devices. An operator typically programs the
system, e.g., via a controller, to transport the sample holders
from device to device as desired for a particular application.
[0071] In addition, the devices typically each have a receiving
module, e.g., for receiving a sample holder. In some cases, the
receiving module couples to a gripper or positioning device on a
robotic arm. In some devices, the sample holder is placed on a
conveyor by the robotic arm or placed in a sample compartment. For
example, the robotic arm optionally opens a door on an incubator
and places the sample holder inside the incubator, e.g., in a plate
carousel.
[0072] The devices used in the systems of the invention include,
but are not limited to, compound storage devices or modules, liquid
dispensers, workstations, replating stations, thermocyclers,
incubators, heating units, pumps, detectors, electrophoresis and/or
chromatography modules, purification and/or filtration modules,
wash modules, centrifuges, PCR modules, vacuums, refrigeration
units, mixing plates, weighing modules, light sources, and other
types of devices known to those of skill in the art. Such devices
are used to perform a variety of techniques including, but not
limited to, PCR, hybridizations, cloning, translation,
transcription, isolations, cell growth, washes, dilutions,
detection, and the like. Some typical devices are described in more
detail below.
[0073] Compound storage devices, such as, specimen plate hotels,
nests, and the like, are optionally included in one or more work
perimeters, e.g., at a station location. For example, an operator
optionally uses one or more plate hotels to introduce a set of
sample holders into the system. For example, an operator optionally
retrieves a set of plates from a long-term storage area, e.g., not
connected to the system; places the plates in a hotel; and
registers the plates with the system, e.g., for inventory purposes.
The operator then typically specifies that the newly introduced
plates should be processed by the system. Alternatively, a storage
system, e.g., a long term storage system, is optionally coupled,
e.g., via a conveyor or rotational robot, to a high throughput
system, e.g., for storage and automatic retrieval and entry into
the system.
[0074] When multiple storage modules are used in the system, they
are optionally identical devices such as those that are
commercially available, or devices specifically configured for a
particular application. For example, compound storage devices are
optionally refrigerated, dehumidified, or maintained under an inert
atmosphere for storing particular types of chemical, genetic,
viral, or cellular material. Other storage devices are optionally
configured to be at substantially room temperature, or to be
warmed, e.g., to 37 degrees centigrade.
[0075] The storage compartments in the present invention typically
have a storage capacity of least about 350,000 samples, at least
about 700,000, or at least about 1,400,000 samples or more. In
addition, other systems and devices are optionally used for storing
and retaining samples, e.g., temporarily or for extended
storage.
[0076] In one embodiment, an incubator or storage compartment of
the invention optionally comprises a housing, which housing has a
plurality of doors. Example storage devices are illustrated by
storage device 235 in FIG. 1. For example, storage device 235
optionally includes two 522 plate capacity carousels, dry nitrogen
for cooling, and "VCR doors" for access. The doors close at least
one opening disposed through at least one surface of the housing.
In addition, the housing includes at least one movable shelf
disposed therein, which shelf is capable of aligning with the
opening. Each of the plurality of doors is independently
accessible, e.g., by a rotational robot of the system. See, e.g.,
U.S. Pat. No. 7,329,394.
[0077] Other devices which are optionally placed in or positioned
on station locations in the present systems include, but are not
limited to, devices for dispensing or transferring liquids or other
reagents, e.g., pin tools, syringes, pumps, and the like. In
addition, a low volume liquid dispensing system is optionally used
in the present systems, e.g., to increase reliability of the
system.
[0078] In high throughput systems, small volumes of liquid are
often used and a need exists to dispense them accurately, e.g.,
into wells, with as little waste as possible, to provide a reliable
system. Such dispensing devices are described, e.g., in U.S. Pat.
No. 6,709,872, entitled "Method and Apparatus for Dispensing Low
Nanoliter Volumes of a Liquid While Minimizing Waste," and in U.S.
Pat. No. 6,659,142, entitled "Apparatus and Method for Preparing
Fluid Mixtures," which are herein incorporated by reference as if
set forth in their entirety.
[0079] In one embodiment, a fluid transfer device of the invention
aspirates a volume of sample into one or more of receptacle from
one or more wells of a multiwell plate which is aligned with the
outlet of the receptacle. A substantial portion of the volume of
the aspirated sample is returned to the well of the multiwell
plate, in which the returned volume of the liquid is less than the
aspirated volume so that a volume of sample is retained in the
receptacle. A portion of the retained volume of sample is
dispensed, e.g., into a well of a second multiwell plate, with any
remaining volume of the retained liquid typically being discarded.
See, e.g., U.S. Pat. No. 6,709,872, for more information.
Typically, the volume of the aspirated sample is at least several
times the volume of the dispensed sample.
[0080] In other embodiments, pin tools are used for dispensing
fluids, e.g., reagents, simultaneously into multiple sample wells.
Pin tools are commercially available, e.g., from V & P
Scientific, Inc., San Diego, Calif. For example, an array of pin
tools that aligns with a plurality of wells in a microwell plate is
optionally used to transfer an aliquot of a sample from wells of
one multiwell plate to wells of another multiwell plate.
[0081] Devices comprising pin tools device also optionally include
one or more wash stations in which the pins are washed between
transfers. For example, after transferring a fluid from one
multiwell plate to another, the pins are optionally washed before
using them for addition of a second reagent, e.g., a different dye
solution, or a different transfer. The present invention also
provides methods of washing a pin array. The methods typically
comprise sequentially dipping an array of pins into a series of
wash solutions, such as DMSO, alcohol, water, and the like.
[0082] Other fluid dispensing devices are also optionally used in
the present invention. For example, at least one sample holder or
assay holder is optionally a multiwell plate with which a fluid
transfer device aligns. The fluid transfer device in this case
typically comprises an array of receptacles arranged such that the
outlets of the receptacles are aligned with a plurality of wells on
the microwell plate, e.g., a 96-well or 384-well plate. The Robbins
Hydra is one example of such a dispensing device. The Robbins Hydra
384 or 96 (Robbins, Scientific, Sunnyvale, Calif.) peripheral
device is an integrated workstation that includes, e.g., 100
microliter syringes. The syringe tips are typically made of the
titanium alloy Duraflex. This peripheral device provides custom
dispensing, e.g., of 50 nanoliter volume samples. Dispensation of
such small volumes is particularly desirable for applications such
as, for example, high throughput protein crystallography.
[0083] Other fluid manipulation devices optionally used in
conjunction with the present systems include those dispensing
systems that incorporate positive displacement pumps and dispenser
valves, e.g., coupled to the pumps. For example, a Cartesian
SynQUAD (available from Cartesian Technologies, Inc., Irvine,
Calif. and described in U.S. Pat. No. 6,063,339) provides an
integrated workstation that dispenses bulk amounts of material,
e.g., about 0.5 to 5.0 microliters of fluid per well of cells or
reagents, at the rate of about one to about two minutes per plate.
The SynQUAD comprises many components that are optionally
positioned on a lab bench or a station location of the present
invention. Pumps typically connect each component to a main module
and to a computer, e.g., with about 80 connections. Software is
optionally installed, e.g., on a supervisor PC, to direct and
control each component. Therefore, the system is readily adaptable
for use in the systems of the invention.
[0084] A multi-drop peripheral device is also optionally placed on
a bench for installation of tubing, e.g., with a preassembled
cassette, for dispensing of material. This device is also
compatible with the robotic system of the present invention.
[0085] Typically, the fluid dispensing and transfer devices of the
invention do not comprise disposable pipette tips. In one
embodiment, the entire system contains no disposable pipette
tips.
[0086] Incubator devices are also optionally used in the systems of
the present invention. For example, an incubator device is
optionally positioned in a station location within a work
perimeter, e.g., work area 110 and station location 380 in FIG. 3.
The incubator is optionally set to provide a desired temperature,
humidity, oxygen, N.sub.2, or CO.sub.2 level, e.g., for
facilitating growth of cellular material. Due to a particular
environment within the incubator, the incubator optionally
comprises a sealed door, provided, for example, by an airlock.
Accordingly, a sealed door preferably has a gripping structure,
which gripping structure is typically configured for coupling to a
robotic gripper on the robotic arm of a robot, e.g., in the same
work perimeter. In such a manner, the robotic arm positions the
robotic gripper adjacent to the gripping structure and opens and
closes the door. As the robot opens and closes the door, a
temporary holding area positioned adjacent to the incubator is
typically used for temporarily holding a sample holder, e.g., as it
is moved into or out of incubator. In addition, an incubator device
of the invention optionally includes custom VCR doors and one or
more plate carousel. An example incubation system for use in the
present invention is described, e.g., in U.S. Pat. No. 7,329,394,
entitled "High Throughput Incubation Devices (VCR DOORS)."
[0087] Detectors are also typically included in at least one work
perimeter of the invention. These devices are optionally any
detection device or any device used to measure physical properties
of a sample. For example, fluorescence, luminescence,
phosphorescence, x-ray, radio-frequency (RF), electrical or optical
detection, such as IR or UV, electrochemical detection, enzymatic
or binding assays, radioactivity, nuclear magnetic resonance
spectrometry, light scattering, chromatography, or mass
spectrometry, e.g., electrospray MS, are optionally used to
quantify and/or characterize various properties of the sample.
Alternatively, the detection devices are charged-couple devices
(CCD) or bottom scanning devices. In one embodiment, a camera is
used to take images of assay results, in which case, the assay
results are optionally analyzed at a later point in time. This
speeds up the processing throughput because each individual well
need not be scanned in real time. Typically, the camera images are
stored in a digital format. Other detectors, diagnostic tools, or
screening devices known to those of skill in the art are also
optionally used to detect, screen, analyze, or otherwise process
samples in the present systems.
[0088] For example, in cell analysis systems, a variety of
detectors are optionally used, such as a Fluorometric Imaging Plate
Reader system (FLIPR.RTM.), e.g., from Molecular Devices Corp.,
Sunnyvale, Calif. In addition, Chemiluminescent imaging plate
reader is also optionally used (CLIPR.TM.) (Molecular Devices
Corp.). It integrates a high sensitivity CCD camera, telecentric
lens, high precision positioning mechanism, and computer system
with software to control the instrument and record data. In fact,
Molecular Devices makes a whole line of microplate reader systems,
including luminescence microplate readers, fluorescence microplate
readers, absorbance microplate readers that are optionally
incorporated into the systems provided herein. For more on imaging
systems, e.g., high content imaging, see, e.g., WO 00/17643 (PCT
US99/21561).
[0089] An LJL Acquest (Molecular Devices, Sunnyvale, Calif.)
peripheral device is another integrated workstation optionally used
in the present system. It has a multi-mode reader and a modified
nest for robotic access.
[0090] Other devices, include, but are not limited to, a Modified
Form a Incubator, and Custom Compound Storage Carousels.
[0091] Another automated device of for use in the present systems
is a replating system. The device or system is used, e.g., to
replate a plurality of samples from one or more small sample plates
into a single large sample plate. Because the integrity of a
compound collection, e.g., one or more large libraries, and
database is of great importance to most discovery processes,
management of the compounds is an important issue. Therefore, the
present invention also provides a replating system and method for
making the difficult transformation from low density format
microtiter plates to high density microtiter plates. For example,
compounds are optionally transferred or replated from 96 well to
384 well microtiter plates and/or from 384 to 1536 well plates.
This is typically a difficult transformation because it is labor
intensive, there are many steps in which error can be introduced,
it is difficult to track the transformation while at the same time
being important to rigorously track it. The present invention
provides an efficient and flexible method to track the reformatting
of microtiter plates. The system uses visual and readable controls
to track the reformatting and allows the user to verify that the
reformatting was successful. Such a system is optionally included
in the systems provided, e.g., at a station location in one or more
work perimeter. Alternatively, the replating procedure is performed
in combination with a storage module.
[0092] Replating typically involves multiple fluid manipulations.
For example, a fluid dispenser, e.g., a programmable fluid
dispenser, and a pipettor system are optionally used in a replating
device, e.g., to transfer the samples contained in a lower
well-density plate, e.g., a 96-well plate or 384-well plate, to a
plate having more wells, e.g., a 384-plate or 1536-well plate. In
addition to transferring the samples in the smaller sample plate to
the higher well density sample plate, the device also provides
and/or transfers markers or labels to the higher well density
sample plate as explained in greater detail below. A Tecan Miniprep
(Tecan US, Durham N.C.), which comprises an automatic sample
processor, is one example of a device that is suitable for
replating operations.
D. Station Locations
[0093] A "station location," as referred to herein, is an area
within a work perimeter, which area is used to accommodate one or
more devices or sample plates. The station location is a place,
e.g., a table, platform, or location, which is configured to
receive a device, e.g., a fluid dispenser, a plate carousel, a
detector, or the like. Each work perimeter of the invention
typically comprises two or more station locations. For example,
FIG. 3 illustrates various station locations, e.g., station
location, 380, 385, 390, 395, 400, and 405, in work area 110. Each
work perimeter typically comprises two or more station locations,
which station locations optionally comprise one or more device,
e.g., an automated device.
[0094] Typically, each station location comprises one device for a
given assay or process, e.g., a thermocycler, a pump, a fluid
dispenser, an incubator, a storage module, or the like. The devices
will typically remain at a single station location during an entire
process and be accessed, e.g., in any order desired, by the
rotational robots.
[0095] Alternatively, the station locations are adapted to a
particular process before operation of the system, such that every
station location comprises a device of use in the immediate
process. In this manner, the station locations convey a great deal
of flexibility to the system. Each location is typically set up or
configured to receive a device. For example, a controller is
optionally associated with each station location, e.g., for sending
and receiving process information. In addition, electrical
connections are typically provided for each station location, such
that whenever a new device is desired, the hook up at a station
location is easily accomplished. In addition, because the station
locations are not necessarily located along a linear path, e.g., a
conveyor, the alignment problems are decreased as compared to
existing systems.
[0096] In some embodiments, however, one or more station locations
are empty or unused. For example, a station location optionally is
left empty or used as a holding area, as described below. In
addition, some station locations have devices positioned therein
that are not used in a particular process. In that case, the
rotational robots are not instructed to transport the sample
holders to that station location. The location is skipped in the
transport path selected. No time is wasted by having to transport
the sample holders through an unused station. Therefore, the system
provides improved throughput and efficiency.
[0097] In some embodiments, the station locations comprise
platforms, e.g., platforms that are optionally raised and lowered,
e.g., mechanically or pneumatically. In other embodiments, the
station location is merely a designated place on a table or bench
to which a device is optionally affixed. The station locations act
as place holders for devices and are optionally any shape and size
depending on the devices of interest.
[0098] Although high throughput screening system 100, as shown in
FIGS. 1 and 3, only defines a select number of station locations,
more or fewer station locations are optionally defined depending
upon the reach of each robotic arm and the size of selected
devices. Further, station locations are optionally added, moved, or
removed depending on specific application needs. For example, a
given work perimeter optionally includes about 2 to about 10
station locations, more typically about 3 to about 5.
[0099] Because station locations can remain the same irrespective
of what device is positioned in that station location, the high
throughput screening system is easily reconfigured to accommodate a
variety of specific needs. Accordingly, high throughput screening
systems of the invention are optionally reconfigured to add,
delete, or replace devices in any station location. Advantageously,
station locations are also optionally added or removed to
accommodate changes in the area or robot orientation. Not only is
the system thereby flexibly reconfigurable, but the system easily
adjusts to accommodate adjustments in work flow.
[0100] In addition, to station locations, each work perimeter also
optionally comprises holding areas, e.g., temporary holding areas,
e.g., for storing sample holders until needed in a particular
assay. For example, FIG. 1 illustrates holding areas 245 and 250 in
work area 130 and holding areas 255 and 260 in work area 110.
Holding areas 255 and 260 in FIG. 1 are shown with sample holders
210 and 205 positioned therein. The holding areas are typically
used to temporarily position a sample holder. These holding areas
optionally contain nest devices such as static exchange nests or
interchange platforms. Other devices that are optionally employed
in temporary holding areas are also contemplated within the present
invention. In one embodiment, one or more of the static holding
areas are used by the operator, e.g., to manually introduce
specimen plates into the system. Fewer or more temporary holding
area devices are optionally used in the high throughput screening
systems of the invention. In fact, the number of holding areas is
variable within the same system and is optionally changed from one
operation to the next.
[0101] In the system illustrated in FIG. 1, holding areas 245, 250,
and 260 are positioned away from any instrumentation and provide a
temporary resting area, e.g., for a specimen plate. For example,
timing considerations sometimes dictate that a specimen plate
should rest for a period of time, e.g., at a holding area. In
addition, the holding areas are optionally used to carry out one or
more processes. For example, filtration of samples, application of
vacuum pressure, or UV exposure of the samples in the sample
holder, are optionally carried out in a holding area. Also, a
holding area optionally accommodates the temporary holding of a
sample holder when the next sequential device is not yet available.
The robotic system typically retrieves the sample holder from the
temporary holding area and moves it to the next sequential device,
when available, e.g., after processing is complete.
[0102] Typically, the station locations of the invention comprise
one or more devices, e.g., as described above, for processing
samples, e.g., as described in more detail below.
E. Transfer Stations
[0103] A transfer station (or hand-off area) is typically a
location located proximal to two or more work perimeters, e.g., for
transferring samples or sample holders between work perimeters. In
some embodiments, the transfer station comprises one or more
platform for placing the sample, e.g., until an adjacent robot
retrieves it. However, the transfer station is also optionally an
area, e.g., on the system surface or a table surface, in which two
or more robotic arms meet and transfer a sample plate directly from
one arm to the other, e.g., where adjacent robots directly pass a
sample holder from one robot to the adjacent robot.
[0104] In addition to transferring samples from one device to a
second device or from one work perimeter to another work perimeter,
the transfer stations of the invention are also optionally used to
transfer samples from one sample holder to another sample holder,
e.g., in a replating procedure as described in more detail below.
Typically, a sample plate, e.g., containing test compounds for
screening, is transferred from a storage module to a transfer
station. From the transfer station, samples can be transferred to
the adjacent work perimeter. Either the entire sample plate can be
transferred to the next work perimeter, or aliquots samples in the
sample plate can be transferred to an assay plate. For example, the
robot in one work perimeter transfers an assay plate to a transfer
station, which transfer station includes a fluid transfer device
that takes an aliquot of a test sample (from the sample plate) and
puts the aliquot into a well of the assay plate. The plate that
contains the test samples is then put back into a storage
incubator, and the assay plate is subjected to further processing
(e.g., addition of additional reagents, incubation, mixing, etc.).
After the desired length of incubation time, the assay plates are
moved to a detector. The sample plates and the assay plates never
have to leave their respective work perimeters. As used herein, the
"test samples" or "test compounds are typically added to assays to
determine the effect of the test samples on the assays.
[0105] FIG. 1 illustrates two transfer stations. Transfer station
195 is positioned between work perimeter 105 and 115 and transfer
station 200 is positioned between work perimeters 115 and 125. In
the figure, transfer station 195 comprises sample holder 215, which
sample holder is available for pick up by robotic arm 155 or 150.
The robotic arms then transfer the plate to any device or station
location within the associated work perimeter, e.g., work perimeter
105 or 115.
F. Sample Holders
[0106] In the high throughput systems provided, samples are
typically stored, processed, and detected using sample holders. A
"sample holder" is any container that holds or contains one or more
sample, e.g., a dried or fluidic sample. A typical sample holder
comprises a multiwell plate, microtitre plate, or specimen plate,
which terms are used interchangeably herein. Multiwell plates are
typically constructed according to industry standards to have
several individual wells, with each well configured to hold a
sample. For example, plates typically contain 96, 384, 968, or
1,536 wells. The high throughput systems of the invention are
preferably configured to accommodate 96, 384, 968, and/or 1,536
well specimen plates. For example, one work perimeter is optionally
configured to accommodate 384-well plates and a second work
perimeter configured for 1536-well plates. Alternatively, all work
perimeters in a system can be configured for one type of plate
(e.g., 384-well plates of 1536-well plates). In addition, many
other types of sample holders, for example, custom sample holders,
petri dishes, gene chips, assay holders, test tube arrays, vial
arrays, crucibles, reaction vessels, or flasks, are also used with
the present invention.
[0107] "Array holders" typically comprise containers in which assay
are conducted. For example, an assay holder is also optionally a
microwell plate, e.g., one that contains the reagents and/or
components for a particular assay or screen. In the present
invention, a set of assay holders is optionally used in addition to
a set of sample holders. The assay holders typically contain assay
components, into which are added test compounds or test samples,
e.g., from the sample holders. The test samples are added to the
assay holders to determine the effect of the test sample on the
assay results.
[0108] Samples contained within the sample holders typically
include, but are not limited to, biological or microbiological
samples, chemical or biochemical samples, cells, cell extracts,
serum, plant extracts, parts for an electronic or medical devices,
and the like. In some embodiments, the sample holders of the
invention optionally contain one or more library of cDNA molecules,
library of promoters, or library of gene regulatory regions
operably linked to one or more reporter gene. For example, a
library of gene regulatory regions is optionally derived from one
or more genes that are differentially expressed in a cell, e.g.,
depending on the presence or absence of a particular stimulus. For
assays using these types of libraries, see, e.g., U.S. Ser. No.
60/275,266, entitled "Identification of Cellular Targets for
Biologically Active Molecules," filed Mar. 12, 2001; and U.S. Ser.
No. 60/275,070, entitled Genomics-Driven High Speed Cellular
Assays," filed Mar. 12, 2001. For example, U.S. Ser. No. 60/275,070
describes screens designed to identify gene regulatory regions and
methods of producing libraries of gene regulatory regions. U.S.
Ser. No. 60/275,266 describes methods for rapidly identifying
targets of any molecule that is biologically active. The methods
involve making a library of cells in which the level of a molecular
target is varied among library members, and identifying those
library members that exhibit a change in response to the test
compound.
[0109] The robotic arms described herein are optionally configured
to hold, e.g., for transport, any type of sample container useful
for the assays of interest. In addition, the robotic arms typically
comprise a gripper mechanism for lifting sample holders. The
gripper mechanism is typically configured to hold the various size
multiwell plates, e.g., including, but not limited to 1536-well
plates. Gripper mechanisms are described, e.g., in U.S. Pat. No.
6,592,324, entitled "Gripper Mechanism."
[0110] To reduce contamination and evaporative effects, it is
sometimes desirable to provide at least some of the sample holders
with lids. A lid that sufficiently seals a sample holder not only
reduces evaporation and contamination, but allows gases to diffuse
into sample wells more consistently and reliably. Lids generally
have a gripping structure, such as a gripping edge, that the
robotic arm gripper engages. Accordingly, a robot is able to lid
and delid the specimen plate as needed. Copending U.S. patent
application Ser. No. 09/569,325 entitled "Specimen Plate Lid and
Method of Using", filed May 11, 2000, now U.S. Pat. No. 6,534,014
discloses a specimen plate lid for robotic use, and is incorporated
herein by reference as if set forth in its entirety. In one
embodiment, the sample holder lids, e.g., stainless steel lids,
comprise a cover having a top surface, a bottom surface, and a
side. In addition, an alignment protrusion extends from the side of
the cover, e.g., positioned to cooperate with an alignment member
of a multiwell plate. The lids further comprise a sealing perimeter
positioned on the bottom surface of the cover, wherein the
alignment protrusion facilitates aligning the lid to the plate so
that a seal is compressibly received between the sealing perimeter
and a sealing surface of the multiwell plate. The lids are of
sufficient weight to compress the seal and form a tight seal
between the lid and the plate. For example, the lids typically
weigh between about 100 grams and about 500 grams. A lidding and/or
de-lidding station is also optionally included as a device in the
present systems, e.g., to add and/or remove the lids described
above to or from the sample holders. Alternatively, the entire
robotic system is optionally enclosed, thus creating a controlled
environment, to further reduce contamination and evaporative
effects.
[0111] In some embodiments, the high throughput processing systems
of the invention include one or more automated systems for
precisely positioning an object, as described in U.S. Ser. No.
09/929,985, entitled "Automated Precision Object Holder and Method
of Using," filed Aug. 14, 2001. Microtiter plates must be placed
precisely under liquid dispensers to enable a liquid dispenser, for
example, to deposit samples or reagents into the correct sample
wells. A tolerance of about 1 mm, which can sometimes be obtained
by systems that do not include this type of automated precision
object holder, is adequate for some low density microtiter plates.
However, such a tolerance is often unacceptable for high density
plates, such as a plate with 1536 wells. Indeed, a positioning
error of one mm for a 1536 well microtiter plate could cause a
sample or reagent to be deposited entirely in the wrong well, or
cause damage to the system, such as to needles or tips of the
liquid dispenser. Accordingly, positioning devices as described in
U.S. Ser. No. 09/929,985 are also optionally included in the
systems of the invention, particularly when 1536 well plates are
used.
[0112] These positioning devices have at least a first alignment
member that is positioned to contact an inner wall of the
microtiter plate when the microtiter plate is in a desired position
on the support. An inner wall 88 of a microtiter plate is shown in,
for example, FIG. 13. In some embodiments, two or more alignment
members are positioned to contact a single inner wall of the
microtiter plate when the microtiter plate is in the desired
position on the support. The use of an inner wall of the microtiter
plate as an alignment surface greatly increases the precision with
which the microtiter plate is positioned on the support compared
to, for example, aligning the microtiter plate using an outer wall,
thereby facilitating further processing of the samples contained in
the microtiter plate. The positioning devices can further include
at least a second alignment member that is positioned to contact a
second wall of the microtiter plate when the microtiter plate is in
the desired position on the support. This second wall is preferably
an inner wall of the microtiter plate. The positioning devices can
include: a) a first pusher for moving the plate in a first
direction so that a first alignment surface of the object contacts
a first set of one or more alignment members; and b) a second
pusher for moving the plate in a second direction so that a second
alignment surface of the object contacts a second set of one or
more alignment members. In presently preferred embodiments, either
or both of the pushers includes a lever pivoting about a pivot
point. The lever can be operably attached to a spring or
equivalent, which causes the pusher to apply a constant force to
the object to, for example, move the object in the first direction
against the first set of alignment members. FIG. 14 illustrates the
positioner in operation, including the use of alignment tabs 30.
For further information, see, U.S. Ser. No. 09/929,985.
[0113] The automated precision object holders can also include a
retaining device for retaining a microtiter plate in a desired
position on a support. These retaining devices can include, for
example, a vacuum plate which, when a vacuum is applied, holds the
microtiter plate in the desired position. The vacuum plate, in some
embodiments, has an interior surface and a lip surface, with the
interior surface being recessed relative to the lip surface.
[0114] Sample holders, e.g., empty multiwell plates or sample
holders comprising a plurality of samples, are typically introduced
into the system in one of two ways. First, they are optionally
manually placed into an incubator and registered in the system,
e.g., at a controller PC. Second, they are optionally introduced
from a static plate hotel, e.g., that is also used for plate
queuing during operation of the system.
[0115] In some embodiments, sample holders are labeled with at
least one identifier or label, for example, a bar code, RF tag,
color code, or other label. When the sample holders are labeled
with a bar code, each robot is typically provided with a bar code
reader. The bar code readers are optionally positioned on the
robotic arms or any other position on the robot depending upon the
application and type of sample container used. By identifying each
specimen plate with a bar code, RF tag, or color code, the system
can positively identify each sample holder, e.g., when retrieving,
processing, or detecting each sample. In addition, the information
is also optionally used to provide reports regarding assay outcomes
and results, and to provide an inventory of a large number of
samples, e.g. libraries of nucleic acid samples. For example, an
inventory is optionally used to compare a list of desired plates
with a list of plates present in the system, and notify an operator
of any discrepancies.
[0116] Advantageously, when a sample holder is provided with a bar
code at opposite ends, and the bar codes have indicia relating
orientation, the present invention determines which end of the
sample holder is facing the robot. For example, one end of the
sample holder optionally has a bar code with an even code, while
the opposite end of the sample holder has an odd numbered code.
Accordingly, the robots of the invention easily determine whether a
leading or trailing edge of a sample holder is facing the bar code
reader in the robot. More advantageously, in this example, the
robot reliably and consistently determines which end of a sample
holder to insert into each device.
[0117] Because compound management is a fundamental part of any
research institute, the integrity of the compound collections and
the databases is important. Therefore, the bar codes described
above or other markers or labels affixed to the sample holders are
optionally used to provide a compound or sample plate inventory,
e.g., that is tracked by a controller module, for the high
throughput processing systems of the invention. The inventory
typically keeps track of what samples and/or sample holders are in
the system, as well as their location and status within the system.
By providing a bar code system on the sample plates, the robotic
arms are used to track the plates throughout the system. In
addition, information can be transferred to a central controller,
e.g., a PC, that coordinates locations with resulting data from
various processes to provide an inventory combined with assay
results.
[0118] Further to providing a complete inventory of samples, the
present invention provides a method for plating materials using
markers to track the plating procedure. For example, samples, e.g.,
libraries of samples, often enter the system in a 96-well format
and are subsequently condensed into a single 384 or 1536-well
plate. To aid in the inventory and tracking process, the
transformation from a low-density format to a high density format
is tracked using markers as described below.
[0119] The system described below is typically used for the
specific application of condensing the contents a first set of
microwell plates into a second set of microwell plates. Typically
the number of wells in the second set is a whole number multiple of
the number of wells in the first set of plates. For example, four
unique 96-well plates are optionally condensed into a single
384-well plate in a method comprising tracking the reformatting to
insure accuracy, e.g., 100% accuracy, e.g., in locating and
tracking samples. The concept also applies to 384 to 1536
transformations and reverse processes. The accuracy of the database
depends on knowing exactly where each 96-well plate is located
within the 384-well plate after the transfer is completed. By
giving the operator a simple visual check as well as providing a
detector check system, the method ensures tracking accuracy.
[0120] Compounds provided in 96-well plates are typically in an
88-well format with one column empty, e.g., column 12. One column
is typically kept empty so that when compounds are assayed there
are blank wells, e.g., for assay controls. The entire column is not
typically needed for controls but it is the standard way of plating
compounds. Also used is an 80-well format in which two columns,
e.g., the first and last columns 1 and 12, are left open.
[0121] The process typically starts with samples, e.g., samples
stored as dry films or fluidic samples, in one or more 96-well
plates in the 88-well format described above. Typically, four
96-well plates are converted up to a single 384-well plate. A
marker is than added to one or more of the empty wells, e.g., well
A12, in the first 96-well plate. See FIG. 11A ands 11B for labeling
of wells and marker wells. The second plate receives a second
marker or label, e.g., in well A12 also. The third and fourth
plates, if they are used, also receive a marker in the similarly
located well in those plates, e.g., well A12. Each marker used is
different, e.g., a different colored dye, a different fluorescent
dye, or a different concentration of fluorescent dye. The contents
of the four plates (or fewer if that is the case) are added
sequentially into the larger plate. If dried films are used in the
smaller plates, they are typically dissolved in the smaller plates
prior to transfer to the larger plate. In the larger plate, e.g.,
the 384-well plate to 1536-well plate, a pattern of markers
results, e.g., in the upper right corner, such as in wells A23-24
and B23-24. In this manner the accuracy of the transfer is
monitored. When a colored dye is used, the process is optionally
monitored visually to ensure accuracy by observing whether the
intended pattern is obtained. If fluorescent dyes are used, a
fluorescent detector is used to monitor whether the plates were
accurately transferred. In some embodiments, a fluorescent dye is
used in combination with a colored dye to allow visual as well as
instrument tracking of samples. In other embodiments, wells other
than A12 are used for markers. Any well may be used as long as the
resulting pattern is predetermined to track the transfer.
[0122] In one example, a solution of colored dye, e.g., about 0.5
mg/ml, plus a florescent dye is added to well A12 in each 96-well
plate. The first plate in the transformation receives a red dye and
a fluorescent dye at concentration lx. The second plate receives a
yellow dye with a fluorescent dye concentration of 0.5.times., the
third plate receives a green dye and a fluorescent dye at
0.25.times.. Finally the fourth plate receives a blue dye and a
fluorescent dye at 0.125x. For example, the dye concentration is
optionally an FITC solution ranging in concentration from about 0.1
mg/ml to about 0.0125 mg/ml. The contents of the four plates are
then added in sequence to a single 384 well plate. In the final 384
well plate a colored pattern is formed in the upper right corner
(e.g., wells A23-24, B23-24), as shown in FIGS. 11 and 12. For
example, FIG. 11 illustrates four 96 well plates with markers,
which are then replated into a 384-well plate as shown in FIG. 12A
and then four 384-well plates are optionally replated in a
1536-well plate, e.g., in a format as shown in FIG. 12B. Each
pattern in the figures is indicative of a different type of dye in
the well as shown in the figure legends. As illustrated in the
figures, the colors allow for the human eye to monitor the process
to ensure accuracy. A simple check to determine the orientation of
the colored dyes allows an operator to be sure of the plate
orientation. The fluorescent dye is detected by one of various
fluorescent detection instruments and allows the plating procedure
to be monitored by instrumentation.
[0123] In some embodiments, the samples from one or more plates are
to be mixed with the corresponding sample in one or more additional
plates. In this case, the mixing can be monitored by determining
the color of the dye in the marker well of the target plate. For
example, if a first plate has a yellow marker and the second plate
has a red marker, when the markers are mixed, the corresponding
well in the target plate will have an orange marker. Similarly, if
the markers are fluorescent dyes of different concentrations, the
target plate will have a concentration of dye can be determined
based on the amounts in the original plates and the dilution
factor.
[0124] In the systems of the present invention the markers can be
dispensed into a sample plate at one station location, e.g.,
comprising a fluid dispenser, and typically transferred into a
higher well density plate, e.g., at the same station location or at
a different location. The plate having the higher well density is
then typically transferred to a detection station location, e.g.,
in the same or a different work perimeter to detect the resulting
color and/or fluorescent pattern in the larger plate, e.g., the 384
or 1536-well plate. In addition, a color photograph is optionally
taken or an operator optionally views the resulting larger plate to
ensure the correct color pattern. Alternately, a colorometric
detector is used.
[0125] Although the high throughput systems of the invention are
primarily automated robotic systems, certain functionality is
optionally manual. For example, an operator optionally manually
introduces a particular sample holder into a high throughput
screening system, e.g., by placing the sample holder onto a table
device, holding area, or the like. For example, holding areas 240
and 250 in FIG. 1, are optionally used to manually introduce a
sample holder into the system, e.g., into work perimeter 105 or 115
respectively. A rotational robot arm optionally retrieves the
sample holder from the manual holding table or area. It is
optionally moved to a storage or station location, or moved to a
transfer area, such as transfer area 195 or 200, e.g., to be
retrieved by a second rotational robot. The rotational robot that
retrieves the sample plate from the holding area or transfer
station typically moves the sample holder into any of its
associated station locations, to be operated on or processed by the
device associated with that station. For example, a rotational
robot positions a sample holder in one of the detectors included in
the system or deposits the plate into a receptacle for a dispensing
device. To facilitate such manual operation, the operator typically
uses a basic command set to introduce, move, and process individual
sample holders. Any combination of manual and automated processes
is contemplated within the present invention. However, sample
holders are also optionally introduced into the system
automatically, e.g., from a storage module within the system or
coupled to the system. In this case, a central controller or a
controller coupled to the storage module is used to direct which
sample holders are introduced into the system.
G. Controllers
[0126] The high throughput screening systems of the invention
typically operate under control of one or more computer systems.
For example, a control unit is optionally coordinated with the
operation of the high throughput system. Alternately, a single
computer or multiple computers are optionally used to control and
monitor the entire system or a desired portion of the system.
Operator stations, e.g., including alerts, are also typically
provided to allow an operator to control and/or monitor the
system.
[0127] For example, FIG. 1 illustrates a control unit 320, which is
optionally used to coordinate the operation of high throughput
screening system 100. As operator monitoring is typically desired
for such a system, an operator station, e.g., station 310 is also
provided. Operator station 310 optionally accommodates, for
example, operator console 315 for monitoring computer and process
functionality, and operator alert 325, e.g., for alerting an
operator with either a visual, audio, or pager alert. The operator
console indicates, for example, what station locations and/or
devices are occupied, what transfer stations are occupied, robot
status, incubator status, temperature of various system components,
and any other information the operator wishes to know about the
system.
[0128] Operator alert 325 is optionally an automated paging system
that pages one or more operators upon notice of an error condition,
e.g., requesting operator intervention. Alternatively, the alert is
a visual or an audible alarm. For example, a telephonic system
allows a control PC to initiate calls to predetermined numbers,
e.g., to telephone or pager numbers. For example, if an error
condition develops during operation, the system calls a number from
a predetermined list of contacts, plays a recorded message and
waits for a telephone keypad response. In this manner, the system
is optionally controlled and kept in operation from a remote
location. The system can also include one or more cameras, e.g., a
webcam, which allows the operator to view the system remotely. This
can allow the operator to troubleshoot the system from a remote
location.
[0129] Preferably, operator station 315 is located adjacent to one
or more work perimeters, such as work perimeters 105, 115, and/or
125. In such a manner the operator not only sees operator console
315 but is also able to visually inspect robotic activity and the
devices of the invention. Accordingly, components of operator alert
325 may be placed in a work perimeter or even on the devices
themselves. The work perimeters are also optionally positioned
distant from the operator and the operator console, with the
operator alert operating to page the operator.
[0130] Referring now to FIG. 2, an example of interconnecting
controllers in high throughput screening system 100 is provided.
Automated instrument devices typically have an integral controller
or a controller assigned to operate that instrument device. For
example, instrument device 225 is shown with integral controller
345, instrument device 265 is shown with integral controller 365,
and instrument device 270 is shown with integral controller 370.
Also, instrument device 230 is shown with a separate dedicated
controller 350, and in a similar manner, instrument device 280 is
shown with separate dedicated controller 360. For some instrument
devices, a single controller operates more than one instrument
device. For example, instrument devices 290 and 285 are shown under
the control of controller 355. Any controller devices and
configurations known in the art are contemplated within the present
invention.
[0131] The controllers not only operate the devices of the
invention, but also typically off-load processing from a system
controller, e.g., controller 320. For example, in one embodiment,
instrument device controllers collect and analyze data and send
summary data information to a system controller. In such a manner,
data communication requirements and bandwidths are reduced, thus
requiring lower speed and therefore less costly communication
connections. Some instrument devices, such as instrument device 235
and instrument device 295, optionally do not have a separate
station controller, but are instead controlled directly from a
system controller, e.g., controller 320. Also, an individual
station optionally takes direction and passes data to more than one
controller. For example, instrument device 235 optionally receive
operational direction from robotic controller 330, but also passes
data back to the central controller 320.
[0132] Although most of the communication links shown in FIG. 2 are
shown as point-to-point connections, other types of connections are
optionally used, such as network, Ethernet, wireless, or multi-drop
connections, such as the multi-drop connection shown between system
controller 350 and system controller 345. Further, instrument
device and system controllers can be physically configured and
connected in other arrangements known to those of skill in the
art.
[0133] Preferably, each rotational robot has its own robot
controller. For example, robot controller 330 controls robot 135,
robot controller 335 controls robot 140, and robot controller 340
controls robot 145. Although FIG. 2 shows each robot controller
directing a single robot, a single robotic controller also
optionally controls multiple robots. Conversely, multiple robotic
controllers can cooperate to control a single robot, e.g.,
controlling a carousel and reach associated with each robot. For
example, robotic controller 330, which is primarily responsible for
controlling robot 135, optionally accepts input from robotic
controller 335 which can effect robotic movements. The robotic and
system controllers are also optionally configured in other physical
and logical arrangements.
[0134] In the example illustrated in FIG. 2, each robotic
controller 330, 335, and 340 is preferably connected to system
controller 320. System controller 320 is connected to operator
console 315 located at operator station 310. System controller 320
also communicates to operator alert 325. Operator alert 325 is, for
example, an automated paging system that pages one or more
operators when an error condition occurs. Further, operator alert
325 optionally includes lights and audible signals for providing
warnings and alerts to operators and technicians in the area. For
example, a light bar having color-coded lights is optionally
positioned adjacent to key devices. In such a manner, an operator
receives a quick visual indication of process status.
[0135] Further, system controller 320 accepts instruction and
passes data to other systems, e.g., via central system link 375.
This link is optionally an internet link, a wireless link, or a
local area network link such as an Ethernet system. Other links,
e.g., electronic, optic, magnetic, or otherwise known in the art,
are used to link system controllers. Advantageously, system
controller 320 provides input to a centralized control and data
collection facility and receives software and operational updates
from a remote source. For example, establishing a web link provides
alert and status information.
[0136] In one embodiment, the system and robots are typically
programmed in AIM and/or V+. Each robot typically has a controller
that is typically DeviceNet and Ethernet compatible. For example,
the controllers are accessed via DeviceNet back to a Controller PC,
which is typically a Pentium III, IV, or other appropriate, e.g.,
faster, computer known to those of skill in the art. In addition to
motion of the robot, the robot controllers are responsible for all
motion within a designated work perimeter or station.
[0137] Software for the PC is typically written in Microsoft Visual
C++, e.g., version 6.0, or other programming language known to
those of skill in the art. The controller PC is typically used to
coordinate the entire system, e.g., providing high level
coordination that reports and acknowledges all faults and/or
errors, and provides user interface functionality. The PC also
typically acts as a data concentrator, recording all data, e.g., in
an Oracle format, and optionally processing such data.
Alternatively, the data is stored for future processing, e.g., on
another PC.
[0138] The controllers and controller links described above are
used with any system as described above or those examples provided
below. In addition, various methods of using the system and the
controllers are discussed below.
H. Example Systems
[0139] In the embodiment illustrated in FIGS. 1-7, high throughput
screening system 100 includes three work perimeters. The first work
perimeter 105 is generally directed to the task of storing samples
or compounds. The second work perimeter 115 is generally directed
to processing samples by, for example, adding reagents, shaking, or
incubating. The third work perimeter 125 is generally directed to
analyzing the samples, for example, by detecting the samples, or
measuring physical properties of the samples. Although the
disclosed example has three work perimeters defined, fewer or more
work perimeters are optionally utilized depending upon application
specific requirements. Advantageously, there is no particular order
that must be followed in transporting samples from one work
perimeter to another work perimeter because of the
multi-directional utility of the present invention. For example, a
sample may be processed in work perimeter 105, transported to work
perimeter 125 for detection, and transported back to work
perimeters 105 and 115 for further processing.
[0140] Although each work perimeter is generally directed to a
particular type of task, the functionality for each work perimeter
may overlap with the functionality of other areas. For example, the
area generally directed to storing compounds may also perform
certain functions related to processing, detecting or other type of
sample property determination.
[0141] In the high throughput system 100 disclosed in this example,
samples are typically stored, processed, and detected using
specimen plates, e.g., 96, 384, 968, or 1,536 wells. For example,
plates 210, 205, and 215 as shown in FIG. 1.
[0142] Each disclosed work perimeter 105, 115, and 125 has an
associated rotational robot. For example, work perimeter 105 has
rotational robot 135, work perimeter 115 has rotational robot 140,
and work perimeter 125 has rotational robot 145. Each rotational
robot preferably rotates about its rotational axis close to a full
360 degrees. Further, each robot preferably adjusts vertically and
horizontally to align relatively higher or lower work positions. In
a preferred embodiment, each rotational robot is a Staubli RX-60
robot that is pedestal mounted.
[0143] Preferably, each rotational robot has a robotic arm that
optionally extends or retracts from the robot's rotational axis.
For example, robotic arm 150 and robotic arm 155 are both shown in
FIG. 1 in a moderately extended position. Robotic arm 160, however,
is shown in FIG. 1 in an extended position. Accordingly, each
rotational robot has an associated rotational reach. For example,
robot 135 has rotational reach 105, robot 140 has rotational reach
115, and robot 145 has rotational reach 125. Although the
rotational reach patterns are shown to be generally circular or
oval, the rotational reach can accommodate other geometries.
[0144] A transfer station is preferably positioned between each
adjacent work perimeter. In one embodiment, the transfer station
provides a temporary area for positioning sample holders to
facilitate moving a sample holder in or out of an area. For
example, transfer station 195 is positioned between work perimeter
105 and work perimeter 115. In a similar manner, transfer station
200 is positioned between work perimeter 115 and work perimeter
125. Although transfer stations 195 and 200 are shown centered
between adjacent work perimeters, the transfer station may be
relatively closer to, or even within, a work perimeter. The
transfer area is also optionally positioned where adjacent robots
directly pass a sample holder from one robot to the adjacent
robot.
[0145] Preferably, each robotic arm has a robotic gripper. For
example, robotic arm 150 has gripper 165, robotic arm 155 has
robotic gripper 170, and robotic arm 160 has robotic gripper 175.
In this disclosed example, each robotic gripper 165, 170, and 175
is configured to removably couple with a specimen plate, such as
standard 384 or 1,536 well plates. Robotic arms 150 and robotic
grippers 170 are optionally operated pneumatically, magnetically,
or by other means known in the art.
[0146] The robotic grippers of the embodiment illustrated in FIG. 1
are configured to removably couple to specimen plates, such as
specimen plates 205, 215, and 220. To transfer between adjacent
work perimeters, a first robot retrieves a specimen plate,
positions the plate into a transfer station, and then a robot from
an adjacent work perimeter retrieves the plate from the transfer
station. For example, FIG. 1 shows sample plate 215 positioned in
transfer station 195. Accordingly, either robot 140 or robot 135
can engage and use specimen plate 215. In a similar manner, FIG. 1
shows robot 145 either returning specimen plate 220 to transfer
station 200 or retrieving specimen plate 220 from transfer station
200 and transporting specimen plate 220 for further processing,
measurement, or detection.
[0147] Work perimeter 115 also provides incubator device 290 which
can be, for example, set to provide the proper conditions for
facilitating growth of cellular material. Due to the particular
environment within the incubator, the incubator may have a sealed
door 300, provided, for example, by an airlock. Accordingly, sealed
door 300 preferably has a gripping structure 305 coupled to robotic
gripper 170. In such a manner, robotic arm 155 can position robotic
gripper 170 adjacent to the gripping structure 305 and open and
close door 300. As the robot must open and close door 300,
preferably a temporary holding area 260 is positioned adjacent to
incubator 290 for temporarily holding a specimen plate as it is
moved into or out of incubator 290.
[0148] In the illustrated embodiment, work perimeter 125, which is
primarily directed to analyzing samples, comprises detector 265 and
detector 270, e.g., fluorescent detectors. After the specimen
plates have been detected in either or both detectors 265 and 270,
the specimen plates are optionally returned to a storage facility,
such as storage facility 230, or may be deposited in a container
device 275 for disposal or reuse.
[0149] Referring now to FIG. 3, the specific configuration of a
variety of work perimeters will be further addressed. In the
illustrated example, high throughput screening system 100 provides
configuration flexibility by, for example, providing a plurality of
station locations within each work perimeter. For example, work
area 110 contains station locations 380, 385, 390, 395, 400, and
405. Work area 120 includes station locations 410, 415, 420 and
425, while work area 130 contains station locations 430, 435, 440,
445, 450, and 455. Although high throughput screening system 100
only defines a select number of station locations, more or fewer
station locations are optionally defined depending upon the reach
of each robotic arm and the size of selected devices. Further,
station locations are optionally added, moved, or removed depending
on specific application needs.
[0150] Devices for performing process steps are typically selected
according to specific application requirements. After selection,
each device is assigned to a particular station location within a
work perimeter. For example, device 225 is assigned to station
location 380, while device 230 is assigned to station location
385.
[0151] Because station locations remain the same irrespective of
what device is positioned in that station location, the high
throughput screening system 100 is easily reconfigured to
accommodate a variety of specific needs. For example, FIG. 3, when
compared to FIG. 1, shows that a new station location 390 was
defined and holds a new storage device 232. FIG. 3 also shows that
station location 400 has been reconfigured to have incubator 237
replace compound storage device 235. Further, work area 120 has had
incubator 290 removed from station location 410. Accordingly, the
high throughput screening system 100 is reconfigured to add,
delete, or replace devices in any station location. Advantageously,
station locations are optionally added or removed to accommodate
changes in the area or robot orientation. Not only is the system
thereby flexibly reconfigurable, but the system easily adjusts to
accommodate adjustments in work flow.
[0152] In another embodiment, the robotic work perimeters are
arranged in a substantially honeycomb configuration that permits a
non-linear processing system 800, as shown in FIG. 8. In this
non-linear processing system, specimen plates 810 are moved, e.g.,
from a first station location 815 to a different station location
815, e.g., in a non-linear fashion. This setup optimizes throughput
of the overall system by permitting sample holders, e.g., specimen
plates 810, to be moved to the closest appropriate station rather
than through a series of stations. In non-linear processing system
800, a plurality of rotational robots 820, are provided, each
having a rotating robotic arm 825 ending with a robotic gripper
830. The robots are positioned within a rotational reach 840 of
each other. The rotational reach 840 of each robotic gripper 830
defines a circle and each robot 820 is positioned so that the
circles defined by the robotic grippers 830 intersect at several
points. At these intersection points and at other points around
rotational reach 840 of each robotic gripper 830, station locations
815 are located. Station locations 815 are configured to accept
specimen plates 810 and/or to conduct procedures or processes on
specimen plates 810. For example, any station location 815
optionally stores, processes, and/or detects the samples in
specimen plate 810. A station location 815 is also optionally used
to perform reagent additions, PCR, purification, filtration,
washing, transfer of samples to new plates, vacuum/pressure
treatment, light/UV exposure, and/or sample removal/addition.
[0153] In non-linear processing system 800, shown in FIG. 8, a
specimen plate 810 moves from one station location 815 to other
station locations in a non-linear fashion thereby allowing a higher
throughput. In addition, this arrangement of rotational robots 820
with accompanying robotic arms 825 and robotic grippers 830 is
optionally used to efficiently assemble devices, e.g., medical
devices or electronic devices. Because process steps sometimes
require a device to be cured, incubated or otherwise processed in a
manner that requires a specific time, a non-linear processing
system 800 optionally comprises nesting stations as part of a
station location 815. In contrast, a linear processing system
requires the device to pass down a linear pathway while it is being
cured or otherwise processed. In a non-linear processing system,
the device can be left at a station location 815 and then when
required, a robotic gripper 830 moves the device to the next
desired station location 815, which is optionally any station
location in the system. In this way, extremely efficient and high
throughput processing systems is provided.
[0154] FIG. 9 illustrates an example high throughput processing
system of the invention. For example, system 900 comprises three
work perimeters, 902, 920, and 940. Each work perimeter is
associated with a rotational robot, e.g., rotational robots 916,
936, and 946. Two transfer stations, stations 918 and 983, are
provided to bridge the area and provide transport between work
perimeters 902, 920, and 940. Work perimeter 902 comprises three
station locations, e.g., 904, 906, and 908. Station location 904
comprises compound incubator 910 and station location 906 comprises
compound incubator 912. A miniprep device, e.g., device 914, such
as a Tecan Miniprep, is positioned in station location 908. Work
perimeter 920 comprises three station locations, e.g., 922, 924,
and 926. Station location 922 comprises assay plate incubator 930
and station location 924 comprises a Hydra 384, device 934. A
Cartesian Synquad, e.g., device 932, is positioned in location 926.
In addition, a Hydra workstation device, e.g., device 928 is
positioned at a station location proximal to both work perimeter
902 and work perimeter 920 and is accessible by either robot 916 or
robot 918. This device can thus function as a transfer station to
transfer sample aliquots from a sample plate in work perimeter 902
to an assay plate in work perimeter 920. A pin tool can also be
used for this purpose in place of the Hydra. Work perimeter 940
comprises two station locations, e.g., locations 942 and 944.
Station location 944 comprises a LJL Acquest plate reader, e.g.,
device 948. Station location 942 is left empty in the example, but
is optionally fitted with a device at any time, e.g., before or
during operation of the device, e.g., as needed.
[0155] Many other embodiments are also available in the present
invention. For example, a system optionally comprises ten station
locations occupied as follows: two compound libraries, 2 plate
interchange platforms or transfer stations, an incubator, 2 liquid
handling devices, 2 plate readers, and a mini-prep station. These
stations are optionally divided into two or three work perimeters.
Other combinations other devices, and different numbers of devices
are also optionally used for various processes, e.g., as described
in more detail below.
[0156] FIG. 10 illustrates the control hardware used for the above
configuration comprising ten stations or devices. In FIG. 10, three
robot controllers are used, e.g., controllers 1006, 1008, and 1010,
one for each robot in the system, e.g., to handle all motion
control. Each robot controller is typically DeviceNet and Ethernet
compatible. Plate carousels and incubators each have a controller,
e.g., first carousel dial 1000, second carousel dial 1002 and
incubator dial 1004. In addition, each piece of peripheral hardware
optionally has its own controller, e.g., with an RS-232 interface
to Device Net. For example, Tecan Mini prep 1014 has liquid
controller 1016 and an RS232 DeviceNet protocol converter, e.g.,
converter 1038. Likewise for Hydra 96 1018 and Hydra 384 1022,
which are controlled via controllers 1020, 1024, with converters
1040 and 1042. A liquid handler is also typically controlled using
its own liquid controller, e.g., Cartesian liquid handler 1026 with
controller 1028 and converter 1044. The plate readers, e.g., 1030
and 1034, are also connected to controllers, e.g., controllers 1032
and 1036 and to the central system via converters 1046 and 1048.
All controllers are accessed, e.g., via DeviceNet, to supervisor PC
1012, which is typically a Pentium III 600 MHz or faster machine.
Other control hardware and devices set ups are also optionally used
in the systems provided. The above is only one of many possible
examples for use in the methods described below.
II. High Throughput Processing Methods
[0157] The present invention provides high throughput processing
systems and methods of using such systems. In general, the systems
above are used to process a number of samples, e.g., simultaneously
or sequentially. Processing typically refers to screening, testing,
building, or the like. For example, a library of drug candidates is
optionally screened or tested for efficacy or an electronic or
medical device is constructed. A typical process comprises
screening a number of a biochemical or chemical compounds.
[0158] The samples are typically contained in sample holders, such
as microwell plates or specimen plates, which are transported
through the system by rotational robots. For example, a robot
optionally retrieves a sample plate from a storage module in a
first work perimeter, transports the sample holder to a second work
perimeter for processing and then to a third work perimeter for
detection and analysis.
[0159] The sequence of steps performed in a given process is
typically specified, e.g., by an operator. The order of the steps
need not follow a linear path through the system and need not
involve each device of the system in a sequential manner. Each
device of the invention is optionally accessed as needed and the
devices are optionally used in a non-sequential or random order.
For example, a sample holder is optionally transported from a first
device to a second device to a third device and then back again to
the first device, e.g., for further mixing or incubating prior to
detection, e.g., at a fourth device. In addition, the order
followed for transporting a sample holder through the system need
not be the same each time the system is used. The order is
changeable and is typically directed at the beginning of each
assay, e.g., by an operator. In addition, upon receipt of the assay
status, an operator optionally changes the assay and directs a new
path for a sample holder in response to the information.
[0160] In one embodiment, the invention is used to screen a
plurality of samples. A screen is typically a test that is
conducted on a number of specimen plates, and may include multiple
steps. A screen is performed by operating a defined method on a
given set of specimen plates. Using the high throughput systems of
the invention, an unprecedented amount of samples are optionally
processed and screened simultaneously, serially or in parallel,
including screening arrayed libraries of chemical entities such as
small molecules, combinatorial chemical compounds, synthetics,
natural products, extracts, drugs or drug candidates, nucleic
acids, short oligonucleotides, anti-sense oligonucleotides,
single-stranded DNA, RNA, double stranded DNA, RNA, RNA/DNA
hybrids, triplexes, proteinaceous substances such as wild-type and
synthetic proteins, peptides, both natural and synthetic,
antibodies, Fab fragments, antibody epitopes, constrained peptides,
protein fragments, dominant-negative and dominant-positive
proteins, mutated proteins, synthetically modified proteins, as
well as expressed sequence elements including eukaryotic and
prokaryotic expression cassettes, retroviruses, adenoviruses, CMV,
SV40, Tn10 driven full length cDNAs, DNA fragments, peptides,
truncated proteins, and the like. For example, see e.g., published
PCT application PCT/US98/27233 (WO 99/32619) for information
regarding double stranded RNA molecule (RNAi) methods for
modulating gene expression.
[0161] Samples for these screens are optionally derived from
synthetics derived from laboratories or engineered organisms, as
well as those obtained, extracted, cloned, or expressed from
naturally occurring species including, but not limited to,
mammalian species (e.g., human, mouse, rat, rabbit, goat),
eukaryotes including Drosophila, yeast, C. elegans, prokaryotes
including bacterial strains, and plants such as algae, aloe vera
and arabidopsis, among others. Additionally, the present systems
are useful for screening whole organisms, especially microorganisms
such as bacteria, yeast, c. elegans, and parasites such as malaria,
and viruses (i.e., hepatitis and other flaviridae, retroviruses,
adenoviruses, and viroids). In one embodiment, the present
invention screens combinations of these organisms or entities,
either serially or in parallel to test their influence on a
particular biological test or assay.
[0162] In this manner, any type of screen is contemplated within
the present invention, and in particular, screens for
agonists/antagonists, natural and synthetic, e.g., for G-protein
coupled receptors, kinases, proteases, phosphatases, and
transcription; agonists/antagonists of cellular, neuronal, hepatic,
tumor cell differentiation, and retrodifferentitation;
agonists/antagonists of viral and parasite mechanisms of entry,
replication, exit, and pathogenesis; agonists/antagonists of immune
cell activation, inactivation, energy, migration, or apoptosis; and
agonists/antagonists of protein-protein interactions important in
immunology, cardiovascular, signaling biology, metabolic disease,
diabetes, osteoporosis, and other disease areas, e.g., as
determined by synthetic and engineered reporter readouts using
cell-free, cellular and organismal targets.
[0163] Methods of using the above described systems for a
particular screen are described in more detail below, e.g., methods
of designing and performing screens. For further information on
various types of screens that are optionally carried out using the
systems and methods of the invention, see, e.g., U.S. Ser. No.
60/275,266, entitled "Identification of Cellular Targets for
Biologically Active Molecules," filed Mar. 12, 2001; U.S. Ser. No.
60/275,148, entitled "Chemical and Combinatorial Biology Strategies
for High Throughput Gene Functionalization," filed Mar. 12, 2001;
U.S. Ser. No. 60/274,979, entitled "Cellular Reporter Arrays,"
filed Mar. 12, 2001; and U.S. Ser. No. 60/275,070, entitled
Genomics-Driven High Speed Cellular Assays," filed Mar. 12, 2001.
For example, U.S. Ser. No. 60/275,070 describes screens designed to
identify gene regulatory regions and producing libraries of gene
regulatory regions. U.S. Ser. No. 60/275,148 describes, e.g.,
methods for screening genes for a variety of functions, e.g.,
disease related functionality.
A. Designing a Process for Use in a High Throughput System
[0164] As described above, the systems provided herein are
optionally used for a variety of different processes, e.g.,
screening processes, which are described in more detail below. In
general, the system relies on a modular approach to defining the
process. Such an approach not only enables logical development of
screens, but also facilitates reusability of method modules and
supports rapid reconfiguration of the system. Modular development
of methods provides substantial flexibility in defining process
steps, and facilitates reuse of steps and methods. Accordingly,
FIG. 4 illustrates software architecture, e.g., for a high
throughput screening system. Although other industries also
optionally benefit from other arrangements of a high throughput
system. The embodiment illustrated is primarily directed to
operating screens for biotechnology or biomedical industries. For
example, FIG. 4 shows that screen 470 includes and is defined by
combining information in method module 490 and system variable
module 495.
[0165] Methods are also typically defined in a modular manner, with
a method defining and organizing individual process steps, e.g.,
using rules and directions. More specifically, a method is defined
as if the method were to be executed on a single sample, which
simplifies method definition.
[0166] Preferably, after method steps have been defined, the
operator indicates the sample plates on which the method is to
operate. In a similar manner, the operator optionally defines a
plate or a series of plates on which the method is not to be
operated. This permits the operator to define selected plates for
control plates or as exception plates. Accordingly, defining
methods and screens is a logical and efficient process.
[0167] Typically, a screen is defined by a method or combination of
methods. In FIG. 4, for example, in screen 470, method 490 defines
a set of individual steps 520. Preferably, each step is a discrete
stage in a method, and is usually associated with a specific
device. Because these steps typically operate on specific devices,
the method also optionally incorporates specific device commands
530. In one embodiment, these steps are defined to operate on a
specific class of instruments. For example, steps can be configured
to "dispense 100 nl" or "aspirate 500 nl". Accordingly, each step
is typically defined to address specific desired functionality from
a class of instruments. During execution of the method, a device
drive, e.g., device drive 505, generates the low-level commands
necessary to drive a specific model of the instrument actually
configured into the system.
[0168] For example, FIG. 5 shows an example of an input screen,
screen 600, e.g., for defining a step for an incubator. The screen
uses a graphical user interface and permits the operator to easily
define incubator duration 610, settings 620, dependencies 630, and
alarms 640.
[0169] Steps 520 are optionally combined or arranged, e.g., in one
or more step lists, e.g., step list 545, for performing steps in a
sequential manner. However, the sequential order need not follow a
predetermined order dictated by the physical setup of the devices
in the system. Any device is accessed at any point in the sequence,
thereby allowing the assay alone, rather than the physical setup of
the system, to dictate the sequence of the step list.
[0170] Further, the start or pace of one step optionally depends on
the result of one or more other steps. Therefore, the method allows
dependencies 535 to be declared. In such a manner, the step list is
optionally interrupted or paused until prerequisite dependencies
are met. This not only simplifies defining methods, but also
enables steps to operate in parallel, thereby increasing throughput
efficiency.
[0171] Furthermore, any number of screens and/or methods are
optionally performed simultaneously, serially, or in parallel. For
example, a high throughput system of the invention optionally
performs three screens, e.g., in parallel, operating multiple
methods simultaneously. For example, an operator optionally defines
the three screens with priorities for certain steps. For example,
the operator initiates screen one, which begins with a dispensing
step followed by an incubation step, another dispensing step,
another incubation step, and a detecting step. Screen two includes
a dispensing step, another dispensing step, an incubation step, an
aspirating step and a detecting step. Screen three entails a
dispensing step, a detection step, a dispensing step and another
detection step.
[0172] A controller system typically coordinates the robots and/or
robot controllers to preserve the priorities programmed in each
screen. For example, a specimen plate A is optionally incubating in
screen one. In parallel, a specimen plate B has undergone a
dispensing step and another dispensing step in screen two, and must
wait for the incubation station now occupied by specimen plate A.
The controller system directs the appropriate robot controller to
move specimen plate B to a temporary holding area until specimen
plate A has completed its incubation. In this manner, a specimen
plate C undergoing screen three can utilize the dispensing station
that was formerly occupied by specimen plate B in screen two. As a
result, multiple screens are run at the same time, thus maximizing
the efficiency and throughput of the overall system with minimal
human intervention.
[0173] Referring again to FIG. 4, method 490 not only performs
steps on individual instrument devices, but also accounts for
moving specimen plates between instrument devices, between work
perimeters, and to and from holding areas. Therefore, method 490
includes move/position information 550. FIG. 6 illustrates a
preferred input screen, screen 680, for defining a move step. A
graphical input screen allows the user to select a "from" device
685 from a pull down menu, and a "to" device 690 from another pull
down menu. Preferably, dependencies 695 are typically set such that
they must be satisfied before the move occurs. Typically, moves are
defined from device to device, independent of either devices'
station location. Only later, as the method is compiled or run will
the system associate a physical location with each device so
robotic moves are determined. And thus advantageously, the physical
location of devices can be changed without affecting defined
methods.
[0174] Further, many samples are time, temperature, and moisture
sensitive, so the processing time are typically monitored.
Accordingly, method 490 allows for a default or defined time slice
525. Time slice 525 defines the maximum time that a specimen plate
can be in transition between devices. For example, if the time
slice is set at five minutes, then the maximum time a specimen
plate can be in transport between devices would be five minutes. If
such time is exceeded, then an error condition occurs and the
specific specimen plate would be identified as a reject.
Preferably, this error condition triggers an operator alert.
Alternatively, the rejected specimen plate is moved, e.g., to a
receptacle and/or disposed.
[0175] Screens also optionally consider information captured in the
system variables, e.g., variables 495 in FIG. 4. For example, plate
descriptions 555 define which specimen plates are active in the
system, e.g., and log that information into a central inventory,
and associate specimen plates with particular bar codes, if
present. The plate descriptions 555 can be modified using the
editor 560. Plate descriptions also include such information as the
number of wells and plate dimensions. By editing plate description
555, an operator optionally introduces new plates into the system,
or requests that certain plates be removed from the system.
Further, an operator defines which specimen plates are used in a
particular screen, for example, by setting a range of plates to be
used or setting a location from which top retrieve plates.
[0176] The system variables 495 also optionally contain system
configuration table 565. Preferably, system configuration table 565
associates particular station locations to specific devices.
Accordingly, system configuration table 565 provides the logical
association of a device to a physical location. In a preferred
embodiment, steps are typically defined to operate on devices,
which are logically identified. As long as a device is consistently
identified with the same logical identifier, the device can be
physically positioned in any available physical location. In such a
manner, a device can be moved to a new station location in a rapid
and convenient manner without disturbing the method or developing a
new screen.
[0177] For example, a device is optionally physically moved from a
first physical station location to a second physical station
location. As an illustration, e.g., in FIG. 3, storage device 295
at station location 425 is optionally moved, e.g., 180.degree. in
relation to work robot 140, e.g., to station location 410. Editing
the system configuration table 565 records the physical change,
e.g., now associating station location 410 with device 295. Since
the system controller still identifies the device with the same
logical identifier and not the physical station location, the
process proceeds normally, without having to develop a new screen.
Using system configuration table 565 greatly improves the
flexibility and ease of reconfiguration for the high throughput
screening systems disclosed herein. Alternatively, no configuration
table is used. Instead, each device has a set of Cartesian
coordinates associated therewith and the system is reprogrammed
with a set of points that are associated with the device whenever
equipment is moved. In this manner, the robots are optionally
reprogrammed each time a new device is added at a particular
location and defined station locations are not needed.
[0178] In one embodiment, a method is compiled once a screen has
been completely identified by its method, plate set, and system
variables. During the compiling process, the system controller
preferably performs numerous quality checks on the method and
utilized devices. For example, the compiler checks that the system
has sufficient incubator capacity for the proposed method.
Preferably, the compiler not only checks for circular, conflicting,
or irrelevant step dependencies, but also optimizes the method by
recognizing steps that can operate in parallel. The compiler also
verifies all devices specified in the method are present in the
system, and determines the station locations for each device.
Accordingly, with the physical location of each device known, the
required robotic motions are calculated and sequenced. If errors
are found in the method, the operator is notified and the
compilation optionally aborted.
[0179] Provided the method compiles properly, the screen is bundled
into a schedule 475 that executes. For example, the schedule
executes the appropriate method on the identified specimen plates
and collects and reports data according to specific application
needs. In addition, once the steps, methods, screens, and schedules
are defined, they are optionally rearranged and reused, e.g., to
facilitate the development of new schedules.
[0180] Still referring to FIG. 4, the software architecture also
includes input-output control 465. The input-output control
includes physical connections and logical communication to the
individual instrument devices using instrument device drivers 505.
It also includes network or other links back to the central system
515, and communications to the operator, which optionally include
an operator console and operator alerts. The present inventions
also typically provide input-output to other devices or systems.
For example, the input-output control could provide imaging or
printed output.
[0181] Software architecture 460 also contemplates that errors will
arise on occasion within the screening systems. For convenience,
errors are classified as hard errors 570 or soft errors 580 as
shown in block 500. For example, soft errors can occur when a
robotic gripper fails to couple to a specimen plate after three
tries. Other soft errors may include low fluids in fluid-handling
devices, and humidity or temperature out of range in an incubator.
In one embodiment, such soft error failures require the attention
of an operator, but do not warrant halting the process or rejecting
one or more specimen plates. Therefore, upon detecting a soft
error, the system preferably notifies an operator, such as by
paging the operator according to paging or activating warning
lights or audible signals using an operator alert.
[0182] However, the high throughput screening systems provided may
also experience hard errors 570. Hard errors typically comprise
major system failures such as a broken gripper, a failed robot, or
any situation that substantially affects the process in operation.
For example, a fluid well running dry or a critical error reported
by one of the automated instrument devices would trigger a hard
error. Upon detecting a hard error, the system preferably notifies
the operator via paging or visual and audible alerts using an
operator alert. Alternatively, the system rejects one or more
specimen plates, and dispose of them, e.g., in a disposal
station.
[0183] Preferably, the paging rules define an escalating order of
operator notification. For example, the paging rules typically
define that one or more junior operators be notified for soft
errors, but that more senior operators or managers be notified upon
a hard failure. In another example, the paging rules include time
dependencies so that if an operator does not respond within a given
time period, then another operator is paged. Paging rules are
optionally adjusted and configured according to specific
application requirements.
[0184] Referring now to FIG. 7, a method of defining a screening
process, 700 is shown. Generally, defining a screen includes
defining a process method 705, selecting a set of specimen plates
710 on which to operate the defined method, and scheduling the
screen 715.
[0185] As shown in FIG. 7, the method in block 705 is defined by
creating device steps 720, creating move steps 725, and arranging
the device and move steps into a step list 730. Block 735 defines
any order dependencies. Block 740 associates specific devices with
their respective station locations. Alternative steps are
optionally used in defining the method of block 705. After the
method has been defined in block 705, the method is optionally
compiled as shown in block 745. Compiling the method typically
includes optimizing the method for more efficient operation as
shown in block 750. Further, compiling preferably checks for
dependency errors 755, such as circular, redundant, and irrelevant
dependencies. Also, compiling typically includes checking that all
utilized devices are available in the system as in block 760.
Preferably, the method of defining a screen 700 provides a modular
and hierarchical method of defining screens. Advantageously, the
present invention develops efficient screens, provides reusable
methods, and easily reconfigures or scales high throughput systems
to meet changing production requirements.
[0186] By using the above methods of designing processes and/or
screens, large amounts of compounds are optionally tested in a
relatively short period of time with accuracy, reliability, and
efficiency. For example, about 500,000 samples are optionally
processed in about 1 day to about 4 days. Example processes
designed as described above, e.g., for use with the systems
described above are detailed below.
B. Example Screening Processes
[0187] In one embodiment, a combination of analytical devices, such
as dispensing devices, incubators, and detectors are installed in
various station locations, each device preferably correlating to a
unique and individual logical identifier. Multi-well specimen
plates such as 1,536 well plates are processed robotically and in
an automated fashion, although any size specimen plate is
optionally used. In a particular example, a T-cell activation
antagonist screen is performed. A dispensing device robotically
plates Jurkat cells in specimen plates at a rate of about one to
two minutes per plate. Once robotically transported to another
workstation, another dispensing device dispenses about 50 .mu.l of
liquid into the specimen plates. After subsequent dispensing steps
and an incubation step, a detector analyzes the specimen plates.
Using this method, about 7000 compounds are optionally screened for
T-cell activation in about 70 minutes. This embodiment further
illustrates the integration of commercially available analytical
devices into the present invention in order to easily and
conveniently reap the benefits of all the aforementioned
advantages. Example protocols are provided below.
Loading Plates into Hotel
[0188] Typically, an operator loads a plate storage area with
micro-plates that contain the test compounds. The operator then
typically inputs, e.g., to the supervisor PC, a protocol to load
the plates into an appropriate incubator or compound storage hotel.
The robot individually unloads plates from the plate storage area
and loads them into the appropriate incubator or other compartment,
e.g., storage compartments 910 and 912 in FIG. 9. The robot
associated with that work perimeter scans all the bar codes on the
plates to be loaded, and the hotel locations of the plates.
Plate Replication
[0189] Empty target plates are loaded, e.g., into a first plate
storage area in work perimeter 940, again referring to FIG. 9. The
operator writes the protocol and lists specific library plates to
be replicated. The robot in work perimeter 902 unloads a compound
plate from the hotel and loads it onto the table of a 384 Hydra
928. The robot in work perimeter 940 removes an empty plate from
the plate storage area to transfer station 983, from which the
robot in work perimeter 920 moves it onto the table of a 384 Hydra
workstation 928. The Hydra aspirates a pre-determined volume of
DMSO from the wash reservoir and dispenses it into the empty
(target) plate. The Hydra aspirates a pre-determined volume of
compound from the source plate and dispenses it into the target
plate. The source and target plates are removed from the 384 Hydra
and loaded back onto the appropriate incubators or hotels such as,
for example incubators 910 and 912 in work perimeter 902.
Compound Picking
[0190] The operator enters, e.g., into the supervisor PC, the
specific compounds and volumes to be retrieved from the library.
Empty multiwell plates are loaded into an incubator 930, referring
to FIG. 9. The robot scans all the bar codes on the plates and the
hotel locations to verify the location and presence of these target
plates. The robot in work perimeter 920 unloads an empty plate from
the hotel and loads it onto the Cartesian liquid handler 932. The
robot in work perimeter 902 removes the appropriate compound plate
from a hotel on the dial and loads it onto transfer station 918.
The robot in work perimeter 920 removes the plate from the transfer
station and loads it onto the Cartesian liquid handler.
[0191] The Cartesian aspirates a pre-determined volume of fluid
from the correct well(s) of the compound plate and transfers the
fluid to the target multiwell plate. The compound (source plate) is
removed from the Cartesian and loaded back onto the transfer
station 918. The compound plate is removed from the transfer
station by robot 916 and loaded back into the appropriate hotel or
incubator. After the desired number of target compounds have been
picked (or the protocol completed), the target multiwell plate is
unloaded from the Cartesian and loaded into a hotel or other plate
storage area (e.g., incubator 912) for further use.
Dispensing Cells
[0192] 1536 well assay plates are loaded into the incubator 930.
Robot 936 removes the empty 1536 well assay plate from the
incubator and positions it onto the Cartesian 932. Cells are
dispensed into the wells of the 1536 well assay plate, e.g., with
an approximately 30 second cycle time. Robot 936 unloads the plate
from the Cartesian and places it back into the incubator. The
process is optionally repeated for all 135 plates.
Adding Compound
[0193] In this embodiment, about 540 compound plates are present in
the library plate hotel. Robot 916 loads a library plate from the
library hotel to the Hydra 96 Ultra 928, which functions as a
transfer station between work perimeter 902 and work perimeter 920.
Robot 936 removes a 1536 well assay plate (with cells) from the
incubator 930 and loads it onto the Hydra 96 Ultra 928. Fluid is
aspirated 4 times, e.g., using the 96-dispenser head, from the 384
compound plate and dispensed into the 1536 well assay plate (it
takes approximately 3 min to complete 4 washes and 4 aspirate and
dispenses). Robot 936 removes the assay plate from the Hydra and
loads it back into the incubator 930. Robot 916 removes the
compound plate from the Hydra and loads it back into the library
hotel 912. Typically, robots 936 and 916 load a total of 135 assay
plates and 540 compound plates into and out of the Hydra 96
Ultra.
Incubation
[0194] Assay plates are typically incubated for about 4 hours (plus
or minus 10%), e.g., prior to being removed for imaging. Therefore,
plates are typically being moved to the readers while compounds are
being dispensed into assay plates.
Dispensing Reagent and Plate Reading
[0195] A 1536 well assay plate is removed from the incubator 930
and loaded into the Cartesian 932. One or more reagent is dispensed
into each of the 1536 wells in the assay plate (approx 45 seconds).
Robot 936 removes the plate from the Cartesian and loads it onto
the material handling dial 983. The material handling dial
transports the assay plate from work perimeter 920 to work
perimeter 940. The robot in work perimeter 940 removes the plate
from the transfer station (which, in this case, is a material
handling dial) and loads it into the plate reader 948. Plates are
preferably loaded to the reader in less than about 30 seconds after
dispensing of reagent. The plate is read (approx 5 minutes). After
the plate is read, robot 946 removes the plate from the incubator
and loads it back on the material handling dial. The material
handling dial transports the plate from work perimeter 940 to work
perimeter 920. The robot in work perimeter 920 to returns the
completed assay plate to the incubator. The process is typically
repeated for each of about 135 assay plates.
[0196] When kinetic plate reading is desired, the robot optionally
returns the plates to the plate reader after additional incubation
times. For example, robot 936 removes the plate from the incubator
and loads it into a hotel in work perimeter 940. After 30 minutes
robot 946 removes the plate from the hotel in work perimeter 940
and loads it back into the plate reader 948. The plate is read
(approx 1 minute). After the plate is read, robot 946 removes the
plate from the incubator and loads it into the hotel in work
perimeter 940. After an additional 30 minutes, robot 946 removes
the plate from the hotel in work area 940 and loads it back into
the plate reader. The plate is read (approx 1 minute). After the
plate is read, robot 946 removes the plate from the plate reader
and loads it back on the material handling dial 983. The material
handling dial transports the plate from cell work perimeter 940 to
work perimeter 920.
Dispensing Equipment Process Development
[0197] The operator typically writes a protocol to dispense 5 .mu.l
of cells into one 1536 well plate and then manually loads one or
more 1536 well microplates onto the table comprising a Cartesian
workstation, which automatically dispenses cells into wells of 1536
well plate. The operator optionally manually removes the plate and
visually inspects it. The plate is then typically manually loaded
into a plate reader, which reads the plate. The plate is then
typically removed, e.g., manually.
[0198] One skilled in the art will appreciate that the present
invention can be practiced by other than the embodiments which are
presented in this description for purposes of illustration and not
of limitation, and the present invention is limited only by the
claims which follow. It is noted that equivalents for the
particular embodiments discussed in this description may practice
the invention as well.
[0199] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. For example, all the
techniques and apparatus described above may be used in various
combinations and other uses for the present invention are also
contemplated. In particular, other high throughput processes may
utilize the present invention. Also, the present invention is
optionally employed to assemble electronic devices, medical
devices, or other devices that require multiple assembly steps. In
addition, the present invention can be used to perform medical
testing, chemical synthesis, or any other multiple process
procedure.
[0200] All publications, patents, patent applications, or other
documents cited in this application are incorporated by reference
in their entirety for all purposes to the same extent as if each
individual publication, patent, patent application, or other
document were individually indicated to be incorporated by
reference for all purposes.
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